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annotate macros.xml @ 7:b4f6df8fa89b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
author galaxyp
date Wed, 01 Oct 2025 22:20:54 +0000
parents 59fec1e2a6c3
children
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1 <macros>
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2 <import>msfragger_macros.xml</import>
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3 <token name="@TOOL_VERSION@">23.0</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
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6 <!--
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7 These keys were generated ONLY for use by the Galaxy tool wrapper, and only after
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8 the user has selected agreed to the academic-use only terms in the tool wrapper.
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9 -->
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10 <token name="@MSFRAGGER_ACADEMIC_USE_KEY@">f28c4be2-759b0a11-6c1ea652-1240565a</token>
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11 <token name="@IONQUANT_ACADEMIC_USE_KEY@">b6c0ad83-9a4e8900-3e83d29c-aeba3bfb</token>
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12 <token name="@DIATRACER_ACADEMIC_USE_KEY@">8de4daf3-a090ed0d-0acdb00a-1485d8a7</token>
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13 <xml name="requirements">
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14 <requirements>
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15 <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
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16 </requirements>
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17 </xml>
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19 <!-- TMT-n uses the following n first labels from TMT-18 -->
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20 <token name="@TMT_LABELS@">['126', '127N', '127C', '128N', '128C', '129N', '129C', '130N', '130C', '131N', '131C', '132N', '132C', '133N', '133C', '134N', '134C', '135N']</token>
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21 <token name="@iTRAQ-4_LABELS@">['114', '115', '116', '117']</token>
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22 <token name="@iTRAQ-8_LABELS@">['113', '114', '115', '116', '117', '118', '119', '121']</token>
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24 <!--
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25 User specifies input file format and selects sample files as are included by the scan_inputs macro
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27 User must also supply their own manifest file, a TSV file of the format:
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28 name, experiment, bioreplicate, data type
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29 -->
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30 <xml name="samples">
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31 <param name="inputs" type="data" format="mzml,mzxml,thermo.raw" multiple="true" label="Proteomics Spectrum files" help="All input scan files must be named with one of the following extensions: .mzML, .mzXML, or .raw"/>
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32 <param name="input_prefix" type="text" value="" optional="true" label="File name prefix" help="Names inputs: prefix_rep#.mzXML Leave blank to use History names of inputs">
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33 <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator>
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34 </param>
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35 <param name="manifest" type="data" format="tabular" label="Manifest file" help="TSV file with entries for each input scan file: Name (Name of input Galaxy history item. Extension in the name must be .mzML, .mzXML, or .raw.), Experiment (empty, alphanumeric, or _), Bioreplicate (empty or integer), Data type (DDA, DIA, GPF-DIA, DIA-Quant, or DIA-lib)"/>
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36 </xml>
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38 <!--
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39 Prepares enviroment variables for FragPipe.
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40 -->
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41 <token name="@PREPARE_ENVIRONMENT@"><![CDATA[
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42 env_location="\$(dirname \$(which philosopher))/.." &&
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43 cp -r \${env_location}/share/fragpipe*/ fragpipe_local/ &&
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44 mkdir .cache .config tmp &&
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45 export XDG_CONFIG_HOME=\$(pwd)/.config &&
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46 export XDG_CACHE_HOME=\$(pwd)/.cache &&
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47 export JAVA_OPTS="\$JAVA_OPTS -Djava.io.tmpdir=\$(pwd)/tmp" &&
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48 export LD_LIBRARY_PATH="\$LD_LIBRARY_PATH:/usr/local/lib" &&
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49 ]]></token>
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50
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51 <!--
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52 Prepares input scan files.
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53
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54 Scans and moved to a scan directory and linked.
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56 Annotation files are copied into the scan directory for TMT workflows.
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57 -->
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58 <token name="@LINK_SAMPLES@"><![CDATA[
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59 CWD=\$(pwd | sed 's@/@\\/@g') &&
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60
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61 mkdir -p scans &&
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62 #if $wf.workflow_name == "TMT10" or $wf.workflow_name == "TMT11"
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63 cp -p '$wf.annotation' 'scans/annotation.txt' &&
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64 #end if
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65
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66 sed "s@^@\$CWD/scans/@" $manifest > fp.manifest &&
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68 #for $sf in $inputs
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69 #set $i_name = $ln_name($sf)
7
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71 ## speclib library does not follow links
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72 #if $wf.workflow_name == "DIA_SpecLib_Quant"
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73 cp '$sf' 'scans/${i_name}' &&
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74 #else
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75 ln -s '$sf' 'scans/${i_name}' &&
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76 #end if
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77
0
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78 #end for
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79 ]]></token>
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80
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81 <!--
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82 Prepares input files, excluding database.
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83 -->
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84 <token name="@PREPARE_INPUTS@"><![CDATA[
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85 mkdir -p outputs &&
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86 @CMD_IMPORTS@
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87 @LINK_SAMPLES@
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88 ]]></token>
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89
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90 <!--
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91 Prepares database.
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92
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93 First genericizes unknown sequence headers in the database.
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94 Then adds decoys, or decoys and contaminants depending on user selection.
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95 -->
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96 <token name="@PREPARE_DATABASE@"><![CDATA[
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97 '$__tool_directory__/genericize_db.py' $database_name genericized_db.fas &&
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98
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99 #if str($database_options) != 'none'
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100 philosopher workspace --init &&
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101 philosopher database --custom genericized_db.fas --prefix rev_
6
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102 #if str($database_options) == 'decoy_and_contam'
0
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103 --contam
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104 #end if
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105 --contamprefix &&
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106 ln -s *-decoys-*.fas final_db.fas &&
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107 #else
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108 ln -s genericized_db.fas final_db.fas &&
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109 #end if
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110 ]]></token>
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111
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112 <!--
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113 Prepares outputs.
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114
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115 Creates log file symlink, makes a new directory for "combined" outputs and creates "concatenated" results.
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116 -->
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117 <token name="@PREPARE_OUTPUTS@"><![CDATA[
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118 cd outputs &&
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119
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120 #if $output_options and 'combined_outputs' in $output_options
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121 mkdir combined_outputs &&
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122 find . -name 'combined*tsv' | xargs -I {} mv {} combined_outputs &&
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123 #end if
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124
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125 ## For each category of results - psm, ion, peptide, protein - this loop concatenates results from each sample into a single result.
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126 ## For example, the entries sample1/psm.tsv and sample2/psm.tsv would be combined to concat_psm.tsv, a single psm.tsv header as its first line.
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127 for f in psm.tsv ion.tsv peptide.tsv protein.tsv; do
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128 n=0;
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129 for i in \$(find * -name \${f}); do
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130 d=\${i%/*};
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131 if [[ \$n == 0 ]]; then
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132 awk 'NR==1{printf("Experiment\t%s\n",\$0);}' \$i > concat_\${f};
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133 fi;
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134 awk 'NR>1{printf("'"\${d}"'\t%s\n",\$0);}' \$i >> concat_\${f}; t=\$(echo \${i} | tr '/' '.');
7
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135 if [[ \${i} == \${t} ]]; then
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136 mv \${i} 1.\${i};
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137 else
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138 mv \${i} \${t};
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139 fi;
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140 n=\$((n+1));
0
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141 done;
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142 done
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143 ]]></token>
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144
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145 <!-- Input database for MSFragger -->
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146 <xml name="fragger_database">
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147 <param name="database_name" type="data" format="fasta" label="Proteomics Search Database in FASTA format" help="Generic sequence headers in the input FASTA file that are not formatted according to the UniProt, NCBI, or ENSEMBL formats will be automatically prefixed with '>generic|' to avoid being misinterpreted by Philosopher."/>
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148 <!-- Whether to add decoys and contaminants to the database with Philosopher -->
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149 <param name="database_options"
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150 type="select"
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151 label="Decoys and contaminants"
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152 help="The default decoy prefix is &quot;rev_&quot;.">
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153 <option value="decoy_and_contam" selected="true">Add decoys and contaminants</option>
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154 <option value="decoy">Add decoys</option>
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155 <option value="none">Don't add decoys or contaminants</option>
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156 </param>
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157
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158 <!-- Database may be split into chunks for performance benefits -->
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159 <param name="num_slices" type="integer" label="Split database" value="1" help="The number of chunks in which to split the database."/>
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160 </xml>
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161
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162 <!--
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163 The following macro allows users to select their FragPipe workfow.
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164
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165 For a given workflow selection, the relevant parameter sections are expanded. Options specific to the selected workflow
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166 are passed to the parameter definitions in the expand element.
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167
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168 The Galaxy parameters overwrite a workflow file provided by FragPipe for the selected workflow. As a result, any parameters
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169 that are not defined in the Galaxy tool will fall back on the FragPipe defaults for that workflow. This logic is defined
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170 in the <configfile> element.
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diff changeset
171 -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
172 <xml name="workflow">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
173 <conditional name="wf">
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
174 <param name="workflow_name" type="select" label="Workflow">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
175 <option value="Basic-Search">Basic-Search</option>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
176 <option value="Open">Open</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
177 <option value="Nonspecific-HLA">Nonspecific-HLA</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
178 <option value="LFQ-MBR">LFQ-MBR</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
179 <option value="TMT10">TMT10</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
180 <option value="TMT11">TMT11</option>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
181 <option value="DIA_SpecLib_Quant">DIA_SpecLib_Quant</option>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
182 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
183
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
184 <when value="Basic-Search">
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
185 <section name="msfragger" expanded="false" title="MSFragger Options">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
186 <expand macro="msfragger_default"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
187 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
188 <expand macro="validation"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
189 pep="false"
6
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
190 perc="false"
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
191 boost="true"
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
192 no="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
193 masswidth="5"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
194 clevel="0"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
195 accmass="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
196 decoyprobs="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
197 nonparam="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
198 expectscore="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
199 ppm="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
200 combined_pepxml="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
201 <expand macro="label_free_quantification" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
202 <expand macro="ptm_shepherd" yes="false" no="true" c="true" z="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
203 <expand macro="isobaric_quantification" yes="false" no="true"/>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
204 <expand macro="diann_quantification" yes="false" no="true"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
205 <expand macro="dia_pseuedo_ms2"/>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
206 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
207
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
208 <when value="Open">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
209 <section name="msfragger" expanded="false" title="MSFragger Options">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
210 <expand macro="msfragger_open"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
211 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
212 <expand macro="validation"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
213 pep="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
214 perc="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
215 boost="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
216 no="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
217 masswidth="1000"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
218 clevel="-2"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
219 accmass="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
220 decoyprobs="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
221 nonparam="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
222 expectscore="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
223 ppm="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
224 combined_pepxml="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
225 <expand macro="crystalc"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
226 </expand>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
227 <expand macro="label_free_quantification" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
228 <expand macro="ptm_shepherd" yes="true" no="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
229 <expand macro="isobaric_quantification" yes="false" no="true" bridge="false" pool="true"/>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
230 <expand macro="diann_quantification" yes="false" no="true"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
231 <expand macro="dia_pseuedo_ms2"/>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
232 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
233
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
234 <when value="Nonspecific-HLA">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
235 <section name="msfragger" expanded="false" title="MSFragger Options">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
236 <expand macro="msfragger_nonspecific_HLA"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
237 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
238 <expand macro="validation"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
239 pep="false"
6
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
240 perc="false"
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
241 boost="true"
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
242 no="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
243 masswidth="5"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
244 clevel="0"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
245 accmass="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
246 decoyprobs="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
247 nonparam="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
248 expectscore="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
249 ppm="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
250 combined_pepxml="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
251 <expand macro="label_free_quantification" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
252 <expand macro="ptm_shepherd" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
253 <expand macro="isobaric_quantification" yes="false" no="true"/>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
254 <expand macro="diann_quantification" yes="false" no="true"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
255 <expand macro="dia_pseuedo_ms2"/>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
256 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
257
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
258 <when value="LFQ-MBR">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
259 <section name="msfragger" expanded="false" title="MSFragger Options">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
260 <expand macro="msfragger_LFQ_MBR"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
261 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
262 <expand macro="validation"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
263 pep="false"
6
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
264 perc="false"
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
265 boost="true"
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
266 no="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
267 masswidth="5"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
268 clevel="0"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
269 accmass="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
270 decoyprobs="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
271 nonparam="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
272 expectscore="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
273 ppm="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
274 combined_pepxml="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
275 <expand macro="label_free_quantification" yes="true" no="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
276 <expand macro="ptm_shepherd" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
277 <expand macro="isobaric_quantification" yes="false" no="true"/>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
278 <expand macro="diann_quantification" yes="false" no="true"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
279 <expand macro="dia_pseuedo_ms2"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
280 </when>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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281
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
282 <when value="DIA_SpecLib_Quant">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
283 <section name="msfragger" expanded="false" title="MSFragger Options">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
284 <expand macro="msfragger_dia_speclib_quant"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
285 </section>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
286 <expand macro="validation"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
287 pep="false"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
288 perc="false"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
289 boost="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
290 no="false"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
291 masswidth="5"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
292 clevel="0"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
293 accmass="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
294 decoyprobs="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
295 nonparam="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
296 expectscore="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
297 ppm="true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
298 combined_pepxml="false"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
299 protp_minprob="0.5"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
300 perc_minprob="0.7"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
301 <expand macro="label_free_quantification" yes="false" no="true"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
302 <expand macro="ptm_shepherd" yes="false" no="true" c="true" z="true"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
303 <expand macro="isobaric_quantification" yes="false" no="true"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
304 <expand macro="diann_quantification" yes="true" no="false"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
305 <expand macro="dia_pseuedo_ms2"/>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
306 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
307
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
308 <when value="TMT10">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
309 <expand macro="tmt_options" plex="TMT-10"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
310 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
311
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
312 <!-- TMT11 is not in FragPipe GUI -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
313 <when value="TMT11">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
314 <expand macro="tmt_options" plex="TMT-11"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
315 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
316 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
317 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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318
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
319 <!-- Options for TMT workflows -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
320 <xml name="tmt_options" token_plex="">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
321 <param name="annotation" type="data" format="txt" optional="false" label="annotation file" help=""/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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322 <section name="msfragger" expanded="false" title="MSFragger Options">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
323 <expand macro="msfragger_TMT"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
324 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
325 <expand macro="validation"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
326 pep="false"
6
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
327 perc="false"
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
328 boost="true"
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
329 no="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
330 masswidth="5"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
331 clevel="0"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
332 accmass="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
333 decoyprobs="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
334 nonparam="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
335 expectscore="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
336 ppm="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
337 combined_pepxml="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
338 protp_minprob="0.5"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
339 <expand macro="isobaric_quantification" yes="true" no="false" plex="@PLEX@" level="2" ref_tag="Bridge" mod_tag="none"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
340 <expand macro="label_free_quantification" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
341 <expand macro="ptm_shepherd" yes="false" no="true" token_unimod="false" token_common="true"/>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
342 <expand macro="diann_quantification" yes="false" no="true"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
343 <expand macro="dia_pseuedo_ms2"/>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
344 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
345
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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346 <!-- Generates the FragPipe workflow-->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
347 <xml name="workflow_configfile">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
348 <configfile name="workflow_configfile"><![CDATA[#slurp
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
349 ## Create a fragpipe params dictionary from a file
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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350 #set $comments = []
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351 #set $wfdict = {}
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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352 #set $wfpath = $__tool_directory__ + '/workflows/' + str($wf.workflow_name) + '.workflow'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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353 #set $fh = open($wfpath, 'r')
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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354 #for $line in $fh:
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
355 #if $line.startswith('#')
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
356 #silent $comments.append($line)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
357 #elif $line.strip() != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
358 #set $kv = $line.strip().split('=')
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
359 #if len($kv) < 2
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
360 #silent $kv.append('')
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
361 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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362 #set $wfdict[$kv[0]] = '='.join($kv[1:])
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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363 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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364 #end for
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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365
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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366 #set $wfdict['database.db-path'] = 'final_db.fas'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
367 #set $wfdict['msfragger.misc.slice-db'] = $num_slices
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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368
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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369 ## Get the MSFragger Params (shared with the MSFragger tool)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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370 #set $prefix = $wf.msfragger
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
371
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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372 @MSFRAGGER_PARAM_DICT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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373 #if len($vmods) > 0
7
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374 #set $msfragger_dict['table.var-mods'] = '; '.join([$re.sub('^(.*,)(\d)$','\\1true,\\2',m) for m in $vmods])
0
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375 #end if
7
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galaxyp
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diff changeset
376
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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377 #set $fmod_items = [
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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378 ("add_Cterm_peptide", "C-Term Peptide"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
379 ("add_Nterm_peptide", "N-Term Peptide"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
380 ("add_Cterm_protein", "C-Term Protein"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
381 ("add_Nterm_protein", "N-Term Protein"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
382 ("add_G_glycine","G (glycine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
383 ("add_A_alanine", "A (alanine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
384 ("add_S_serine", "S (serine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
385 ("add_P_proline", "P (proline)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
386 ("add_V_valine", "V (valine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
387 ("add_T_threonine", "T (threonine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
388 ("add_C_cysteine", "C (cysteine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
389 ("add_L_leucine", "L (leucine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
390 ("add_I_isoleucine", "I (isoleucine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
391 ("add_N_asparagine", "N (asparagine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
392 ("add_D_aspartic_acid", "D (aspartic acid)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
393 ("add_Q_glutamine", "Q (glutamine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
394 ("add_K_lysine", "K (lysine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
395 ("add_E_glutamic_acid", "E (glutamic acid)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
396 ("add_M_methionine", "M (methionine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
397 ("add_H_histidine", "H (histidine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
398 ("add_F_phenylalanine", "F (phenylalanine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
399 ("add_R_arginine", "R (arginine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
400 ("add_Y_tyrosine", "Y (tyrosine)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
401 ("add_W_tryptophan", "W (tryptophan)"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
402 ("add_B_user_amino_acid", "B "),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
403 ("add_J_user_amino_acid", "J"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
404 ("add_O_user_amino_acid", "O"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
405 ("add_U_user_amino_acid", "U"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
406 ("add_X_user_amino_acid", "X"),
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
407 ("add_Z_user_amino_acid", "Z")
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
408 ]
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
409 #set $fmod_string = ""
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
410 #for $m in $fmod_items
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
411 #set fmod_var_name = $m[0]
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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diff changeset
412 #set fmod_wf_name = $m[1]
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
413 #set $fmod_bool = $fmod_bools.get($fmod_var_name + "_bool")
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
414 #set $fmod_val = $fmod_vals.get($fmod_var_name)
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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415 #set $fmod_string += "; " + ",".join([str($fmod_val),str($fmod_wf_name),str($fmod_bool),"-1"])
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
416 #end for
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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417 #set $fmod_string = $fmod_string[2:]
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
418 #set $msfragger_dict['table.fix-mods'] = $fmod_string
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
419
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
420 #for $k in $msfragger_dict.keys()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
421 #set $kv = $k + '=' + str($msfragger_dict[$k])
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
422 #set $wfk = 'msfragger.' + $k
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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423 #set $wfdict[$wfk] = str($msfragger_dict[$k])
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galaxyp
parents:
diff changeset
424 #end for
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galaxyp
parents:
diff changeset
425
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
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426 @VALIDATION@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
427 @PTM_SHEPHERD@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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428 @LABEL_FREE_QUANTIFICATION@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
429 @ISOBARIC_QUANTIFICATION@
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
430 @DIANN_QUANTIFICATION@
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
431 @DIA_PSEUDO_MS2@
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
432
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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diff changeset
433 ## These values are specifically set by the GUI when running DIA_SpecLib_Quant
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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diff changeset
434 #if $wf.workflow_name == "DIA_SpecLib_Quant"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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435 #set $wfdict["ptmshepherd.annotate_assigned_mods"] = "false"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
436 #set $wfdict["ptmshepherd.use_msfragger_localization"] = "true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
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diff changeset
437 #end if
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
438
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
439 ## Populate the workflow with configuration and comment dictionary entries populated by tool params.
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
440 #for $comment in $comments
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
441 $comment
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
442 #end for
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
443
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
444 #for $k in sorted($wfdict.keys())
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
445 #set $kv = $k + '=' + str($wfdict[$k])
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
446 $kv
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
447 #end for
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
448 #slurp]]></configfile>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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449 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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450
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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451 <!-- Percolator options -->
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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452 <xml name="percolator" token_perc_minprob="0.5">
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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453 <section name="percolator" expanded="true" title="Percolator">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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454 <param name="keep_tsv_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep intermediate files"/>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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455 <param name="min_prob" type="float" value="@PERC_MINPROB@" label="Minimum probability (default 0.5)"/>
0
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456 </section>
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457 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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458
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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459 <!-- Set Percolator workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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460 <token name="@PERCOLATOR@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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461 #set $prc = $wf.validation.validation_tab.psm_validation.percolator
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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462 #set $wfdict['percolator.run-percolator'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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463 #set $wfdict['percolator.keep-tsv-files'] = str($prc.keep_tsv_files)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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464 #set $wfdict['percolator.min-prob'] = str($prc.min_prob)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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465 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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466
4
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
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467 <xml name="msbooster">
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
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468 <section name="msbooster" expanded="true" title="MSBooster">
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
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469 <param name="predict_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict RT"/>
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
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470 <param name="predict_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict spectra"/>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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471 <param name="predict_im" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict IM"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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472 <param name="use_koina" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Koina server" help="The public server used is https://koina.wilhelmlab.org:443/v2/models"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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473 <param name="find_best_rt_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find best RT model (requires Koina server)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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474 <param name="find_best_im_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find best IM model if applicable (requires Koina server)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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475 <param name="find_best_spectra_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find best spectral model (requires Koina server)"/>
4
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
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476 </section>
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
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477 </xml>
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
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478 <token name="@MSBOOSTER@"><![CDATA[
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
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479 #set $prfx = $wf.validation.validation_tab.psm_validation.msbooster
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
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480 #set $wfdict['msbooster.run-msbooster'] = 'true'
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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481 #set $wfdict['msbooster.predict-rt'] = $prfx.predict_rt
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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482 #set $wfdict['msbooster.predict-spectra'] = $prfx.predict_spectra
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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483 #set $wfdict['msbooster.predict-im'] = $prfx.predict_im
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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484 #if $prfx.use_koina == 'true'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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485 #set $wfdict['msbooster.koina-url'] = 'https://koina.wilhelmlab.org:443/v2/models/'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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486 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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487 #set $wfdict['msbooster.find-best-rt-model'] = $prfx.find_best_rt_model
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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488 #set $wfdict['msbooster.find-best-spectra-model'] = $prfx.find_best_spectra_model
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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diff changeset
489 #set $wfdict['msbooster.find-best-im-model'] = $prfx.find_best_im_model
4
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diff changeset
490 ]]></token>
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
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diff changeset
491
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
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492
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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493 <!-- Philosopher Report (phi-report) options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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494 <xml name="phi_report">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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495 <conditional name="phi_report">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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496 <param name="run_phi_report" type="select" label="Generate Philosopher Reports">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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497 <option value="true" selected="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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498 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
499 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
500 <when value="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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501 <section name="phi_report_opts" expanded="false" title="FDR Filter and Report">
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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502 <param name="dont_use_prot_proph_file" type="boolean" truevalue="true" falsevalue="false" checked="false"/>
0
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503 <param name="print_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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504 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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505 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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506 <when value="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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507 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
508 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
509
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
510 <!-- Set Philosopher Report (phi-report) workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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511 <token name="@PHIREPORT@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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512 #set $prfx = $wf.validation.validation_tab.phi_report
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
513 #if $prfx.run_phi_report == 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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514 #set $wfdict['phi-report.run-report'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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515 #set $prfx = $wf.validation.validation_tab.phi_report.phi_report_opts
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
516 #set $wfdict['phi-report.print-decoys'] = $prfx.print_decoys
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
517 #set $wfdict['phi-report.dont-use-prot-proph-file'] = $prfx.dont_use_prot_proph_file
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
518 #else
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
519 #set $wfdict['phi-report.run-report'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
520 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
521 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
522
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
523 <!-- PeptideProphet options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
524 <xml name="peptide_prophet" token_masswidth="5" token_clevel="0" token_accmass="true" token_decoyprobs="true" token_nonparam="true" token_expectscore="true" token_ppm="true" token_combined_pepxml="false">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
525 <section name="peptide_prophet" expanded="true" title="PeptideProphet">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
526 <param name="combined_pepxml" type="boolean" truevalue="true" falsevalue="false" checked="@COMBINED_PEPXML@" label="Single combined pepxml per experiment or group"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
527 <param argument="--decoyprobs" type="boolean" truevalue="--decoyprobs" falsevalue="" checked="@DECOYPROBS@" label="compute possible non-zero probabilities for Decoy entries on the last iteration"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
528 <param argument="--ppm" type="boolean" truevalue="--ppm" falsevalue="" checked="@PPM@" label="use PPM mass error instead of Dalton for mass modeling"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
529 <param argument="--accmass" type="boolean" truevalue="--accmass" falsevalue="" checked="@ACCMASS@" label="use Accurate Mass model binning"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
530 <param argument="--nonparam" type="boolean" truevalue="--nonparam" falsevalue="" checked="@NONPARAM@" label="use semi-parametric modeling, must be used in conjunction with --decoy option"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
531 <param argument="--expectscore" type="boolean" truevalue="--expectscore" falsevalue="" checked="@EXPECTSCORE@" label="use expectation value as the only contributor to the f-value for modeling"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
532 <param argument="--masswidth" type="float" value="@MASSWIDTH@" label="model mass width (default 5)"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
533 <param argument="--clevel" type="integer" value="@CLEVEL@" label="set Conservative Level in neg_stdev from the neg_mean, low numbers are less conservative, high numbers are more conservative"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
534 <param argument="--glyc" type="boolean" truevalue="--glyc" falsevalue="" checked="false" label="enable peptide Glyco motif model"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
535 <param argument="--combine" type="boolean" truevalue="--combine" falsevalue="" checked="false" label="combine the results from PeptideProphet into a single result file" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
536 <param argument="--minpeplen" type="integer" value="7" label="minimum peptide length not rejected (default 7)" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
537 <param argument="--minprob" type="float" value="0.05" label="report results with minimum probability" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
538 <param argument="--nomass" type="boolean" truevalue="--nomass" falsevalue="" checked="false" label="disable mass model" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
539 <param argument="--nonmc" type="boolean" truevalue="--nonmc" falsevalue="" checked="false" label="disable NMC missed cleavage model" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
540 <param argument="--nontt" type="boolean" truevalue="--nontt" falsevalue="" checked="false" label="disable NTT enzymatic termini model" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
541 <param argument="--phospho" type="boolean" truevalue="--phospho" falsevalue="" checked="false" label="enable peptide phospho motif model" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
542 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
543 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
544 <token name="@PEPTIDEPROPHET@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
545 #set $prfx = $wf.validation.validation_tab.psm_validation.peptide_prophet
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
546 #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
547 #set $wfdict['peptide-prophet.combine-pepxml'] = str($prfx.combined_pepxml)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
548 #set $cmd_opts = [str($prfx.accmass),str($prfx.combine),str($prfx.decoyprobs),str($prfx.expectscore),str($prfx.glyc),str($prfx.nomass),str($prfx.nonmc),str($prfx.nonparam),str($prfx.nontt),str($prfx.phospho),str($prfx.ppm)]
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
549 #silent $cmd_opts.append('--clevel ' + str($prfx.clevel))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
550 #silent $cmd_opts.append('--masswidth ' + str($prfx.masswidth))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
551 #silent $cmd_opts.append('--minpeplen ' + str($prfx.minpeplen))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
552 #silent $cmd_opts.append('--minprob ' + str($prfx.minprob))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
553 #set $wfdict['peptide-prophet.cmd-opts'] = ' '.join($cmd_opts).strip()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
554 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
555
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
556 <!-- CrystalC options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
557 <xml name="crystalc">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
558 <param name="run_crystalc" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Run Crystal-C" help="Recommend for open searches for additional resuts cleanup"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
559 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
560
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
561 <!-- Protein Prophet options -->
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
562 <xml name="protein_prophet" token_protp_minprob="0.05">
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
563 <conditional name="protein_prophet">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
564 <param name="run_protein_prophet" type="select" label="Run Protein Prophet">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
565 <option value="true" selected="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
566 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
567 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
568 <when value="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
569 <section name="protein_prophet_opts" expanded="true" title="Protein Prophet">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
570 <param argument="--iprophet" type="boolean" truevalue="--iprophet" falsevalue="" checked="false" label="input is from iProphet" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
571 <param argument="--maxppmdiff" type="integer" value="2000000" label="maximum peptide mass difference in ppm (default 2000000)" />
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
572 <param argument="--minprob" type="float" value="@PROTP_MINPROB@" label="PeptideProphet probability threshold (default 0.05)" />
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
573 <param argument="--nonsp" type="boolean" truevalue="--nonsp" falsevalue="" checked="false" label="do not use NSP model" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
574 <param argument="--subgroups" type="boolean" truevalue="--subgroups" falsevalue="" checked="false" label="do not use NOGROUPS" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
575 <param argument="--unmapped" type="boolean" truevalue="--unmapped" falsevalue="" checked="false" label="report results for UNMAPPED proteins" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
576 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
577 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
578 <when value="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
579 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
580 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
581
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
582 <!-- Set ProteinProphet workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
583 <token name="@PROTEINPROPHET@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
584 #set $prfx = $wf.validation.validation_tab.protein_prophet
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
585 #if $prfx.run_protein_prophet == 'true'
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
586 #set $prfx = $wf.validation.validation_tab.protein_prophet.protein_prophet_opts
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
587 #set $wfdict['protein-prophet.run-protein-prophet'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
588 #set $cmd_opts = [str($prfx.iprophet),str($prfx.nonsp),str($prfx.subgroups),str($prfx.unmapped)]
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
589 #silent $cmd_opts.append('--maxppmdiff ' + str($prfx.maxppmdiff))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
590 #silent $cmd_opts.append('--minprob ' + str($prfx.minprob))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
591 #set $wfdict['protein-prophet.cmd-opts'] = ' '.join($cmd_opts).strip()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
592 #else
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
593 #set $wfdict['protein-prophet.run-protein-prophet'] = 'false'
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
594 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
595 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
596
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
597 <!-- Validation options. Includes PeptideProphet, Percolator, MSBooster, ProteinProphet, and CrystalC -->
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
598 <xml name="validation" token_expand="false" token_pep="false" token_perc="false" token_boost="false" token_no="true" token_masswidth="5" token_clevel="0" token_accmass="true" token_decoyprobs="true" token_nonparam="true" token_expectscore="true" token_ppm="true" token_combined_pepxml="false" token_protp_minprob="0.05" token_perc_minprob="0.5">
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
599 <section name="validation" expanded="@EXPAND@" title="Validation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
600 <conditional name="validation_tab">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
601 <param name="run_validation" type="select" label="Run Validation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
602 <option value="true" selected="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
603 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
604 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
605 <when value="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
606 <yield/> <!-- crystalc -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
607 <conditional name="psm_validation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
608 <param name="run_psm_validation" type="select" label="PSM Validation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
609 <option value="peptide_prophet" selected="@PEP@">Run PeptideProphet</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
610 <option value="percolator" selected="@PERC@">Run Percolator</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
611 <option value="msbooster_percolator" selected="@BOOST@">Run MSBooster and Percolator</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
612 <option value="no" selected="@NO@">Use workflow values</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
613 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
614 <when value="peptide_prophet">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
615 <expand macro="peptide_prophet" masswidth="@MASSWIDTH@" clevel="@CLEVEL@" accmass="@ACCMASS@" decoyprobs="@DECOYPROBS@" nonparam="@NONPARAM@" expectscore="@EXPECTSCORE@" ppm="@PPM@" combined_pepxml="@COMBINED_PEPXML@"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
616 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
617 <when value="percolator">
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
618 <expand macro="percolator" perc_minprob="@PERC_MINPROB@"/>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
619 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
620 <when value="msbooster_percolator">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
621 <expand macro="msbooster"/>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
622 <expand macro="percolator" perc_minprob="@PERC_MINPROB@"/>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
623 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
624 <when value="no">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
625 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
626 </conditional>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
627 <expand macro="protein_prophet" protp_minprob="@PROTP_MINPROB@"/>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
628 <expand macro="phi_report"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
629 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
630 <when value="false">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
631 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
632 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
633 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
634 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
635
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
636 <!-- Set validation workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
637 <token name="@VALIDATION@"><![CDATA[
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
638 #if $wf.validation.validation_tab.run_validation == "true"
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
639 #set $prfx = $wf.validation.validation_tab.psm_validation
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
640 #if $prfx.run_psm_validation == 'peptide_prophet'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
641 #set $wfdict['run-psm-validation'] = 'true'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
642 #set $wfdict['msbooster.run-msbooster'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
643 #set $wfdict['percolator.run-percolator'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
644 @PEPTIDEPROPHET@
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
645 #elif $prfx.run_psm_validation == 'percolator'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
646 #set $wfdict['run-psm-validation'] = 'true'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
647 #set $wfdict['msbooster.run-msbooster'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
648 #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
649 @PERCOLATOR@
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
650 #elif $prfx.run_psm_validation == 'msbooster_percolator'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
651 #set $wfdict['run-psm-validation'] = 'true'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
652 #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
653 @MSBOOSTER@
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
654 @PERCOLATOR@
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
655 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
656 @PROTEINPROPHET@
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
657 @PHIREPORT@
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
658 #else
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
659 #set $wfdict['run-psm-validation'] = 'false'
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
660 #set $wfdict['msbooster.run-msbooster'] = 'false'
6
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
661 #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
662 #set $wfdict['percolator.run-percolator'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
663 #set $wfdict['protein-prophet.run-protein-prophet'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
664 #set $wfdict['phi-report.run-report'] = 'false'
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
665 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
666 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
667
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
668 <!-- PTM-Sheperd options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
669 <xml name="ptm_shepherd" token_expand="false" token_yes="true" token_no="false" token_a="false" token_b="true" token_c="false" token_x="false" token_y="true" token_z="false" token_unimod="true" token_common="false" token_glyco="false" token_custom="false">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
670 <section name="ptms" expanded="false" title="PTMs">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
671 <conditional name="ptm_shepherd">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
672 <param name="run_ptm_shepherd" type="select" label="Run PTM Shepherd">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
673 <option value="yes" selected="@YES@">yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
674 <option value="no" selected="@NO@">no</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
675 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
676 <when value="yes">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
677 <param name="output_extended" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extended output"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
678 <section name="ptm_profiling" expanded="false" title="PTM Profiling">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
679 <param name="histo_smoothbins" type="integer" value="" min="0" optional="true" label="Smoothing factor" help="ptmshepherd.histo_smoothbins"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
680 <param name="precursor_mass_units" type="select" label="Precursor Mass tolerance units" help="ptmshepherd.precursor_mass_units">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
681 <option value="1" selected="true">ppm</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
682 <option value="0" selected="false">Daltons</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
683 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
684 <param name="precursor_tol" type="float" value="" min="0" optional="true" label="Precursor tolerance" help="ptmshepherd.precursor_tol"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
685 <param name="peakpicking_promRatio" type="float" value="" min="0" optional="true" label="Prominece ratio" help="ptmshepherd.peakpicking_promRatio"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
686 <param name="peakpicking_mass_units" type="select" label="Peakpicking Mass tolerance units" help="ptmshepherd.peakpicking_mass_units">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
687 <option value="1" selected="true">ppm</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
688 <option value="0" selected="false">Daltons</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
689 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
690 <param name="peakpicking_width" type="float" value="" min="0" optional="true" label="Peak picking width" help="ptmshepherd.peakpicking_width"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
691 <param name="peakpicking_minPsm" type="integer" value="" min="0" optional="true" label="Peak minimum PSMs" help="ptmshepherd.peakpicking_minPsm"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
692 <param name="spectra_ppmtol" type="float" value="" min="0" optional="true" label="Fragment Mass tolerance (PPM)" help="ptmshepherd.spectra_ppmtol"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
693 <param name="normalization" type="select" optional="true" label="Normalize data to" help="ptmshepherd.normalization-psms ptmshepherd.normalization-scans">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
694 <option value="psms" selected="true">PSMs</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
695 <option value="scans" selected="false">MS2 scans</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
696 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
697 <param name="varmod_masses" type="select" optional="true" label="Custom mass shifts" help="ptmshepherd.varmod_masses">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
698 <option value="Failed_Carbamidomethylation\:-57.021464">Failed_Carbamidomethylation:-57.021464</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
699 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
700 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
701 <section name="ptm_annotation" expanded="true" title="PTM Annotation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
702 <param name="annotation_tol" type="float" value="" min="0" optional="true" label="Annotation tolerance (Da)" help="ptmshepherd.annotation_tol"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
703 <conditional name="annotation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
704 <param name="annotation_source" type="select" label="Annotation source" help="ptmshepherd.annotation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
705 <option value="unimod" selected="@UNIMOD@">Unimod</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
706 <option value="common" selected="@COMMON@">Common mass shifts</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
707 <option value="glyco" selected="@GLYCO@">Glyco mass shifts</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
708 <option value="custom" selected="@CUSTOM@">Custom annotation file</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
709 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
710 <when value="unimod"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
711 <when value="common"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
712 <when value="glyco"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
713 <when value="custom">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
714 <param name="annotation_file" type="data" format="txt" label="Custom annotation file"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
715 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
716 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
717 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
718 <section name="ptm_localization" expanded="false" title="PTM Localization">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
719 <param name="nions" type="select" multiple="true" optional="true" label="Use specified N-term ions" help="(default: a,b for CID, c for ETD)">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
720 <option value="a" selected="@A@">a</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
721 <option value="b" selected="@B@">b</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
722 <option value="c" selected="@C@">c</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
723 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
724 <param name="cions" type="select" multiple="true" optional="true" label="use specified C-term ions" help="(default: y for CID, z for ETD)">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
725 <option value="x" selected="@X@">x</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
726 <option value="y" selected="@Y@">y</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
727 <option value="z" selected="@Z@">z</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
728 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
729 <param name="spectra_maxfragcharge" type="integer" value="" min="0" optional="true" label="Max fragment charge" help="ptmshepherd.spectra_maxfragcharge"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
730 <param name="localization_allowed_res" type="select" label="Restrict localization to" help="ptmshepherd.localization_allowed_res">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
731 <option value="" selected="true">none</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
732 <option value="all">all</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
733 <option value="N">N</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
734 <option value="ST">ST</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
735 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
736 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
737 <!-- Not yet implemented
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
738 <section name="ion_discovery" expanded="false" title="Diagnostic Ion Discovery">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
739 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
740 <section name="glycan" expanded="false" title="Gyclan Assignment and FDR">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
741 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
742 -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
743 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
744 <when value="no"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
745 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
746 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
747 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
748
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
749 <!-- Set PTM-Sheperd workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
750 <token name="@PTM_SHEPHERD@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
751 #set $prfx = $wf.ptms.ptm_shepherd
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
752 #if $prfx.run_ptm_shepherd == 'yes'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
753 #set $wfdict['ptmshepherd.run-shepherd'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
754 #set $cxt = $prfx.ptm_profiling
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
755 #set $wfdict['ptmshepherd.output_extended'] = $prfx.output_extended
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
756 #if $cxt.histo_smoothbins != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
757 #set $wfdict['ptmshepherd.histo_smoothbins'] = $cxt.histo_smoothbins
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
758 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
759 #if $cxt.precursor_tol != ''
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
760 #set $wfdict['ptmshepherd.precursor_mass_units'] = $cxt.precursor_mass_units
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
761 #set $wfdict['ptmshepherd.precursor_tol'] = $cxt.precursor_tol
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
762 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
763 #if $cxt.peakpicking_promRatio != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
764 #set $wfdict['ptmshepherd.peakpicking_promRatio'] = $cxt.peakpicking_promRatio
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
765 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
766 #if $cxt.peakpicking_width != ''
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
767 #set $wfdict['ptmshepherd.peakpicking_mass_units'] = $cxt.peakpicking_mass_units
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
768 #set $wfdict['ptmshepherd.peakpicking_width'] = $cxt.peakpicking_width
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
769 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
770 #if $cxt.peakpicking_minPsm != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
771 #set $wfdict['ptmshepherd.peakpicking_minPsm'] = $cxt.peakpicking_minPsm
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
772 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
773 #if $cxt.spectra_ppmtol != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
774 #set $wfdict['ptmshepherd.spectra_ppmtol'] = $cxt.spectra_ppmtol
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
775 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
776 #if $cxt.normalization != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
777 #if $cxt.normalization == "psms"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
778 #set $wfdict['ptmshepherd.normalization-psms'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
779 #set $wfdict['ptmshepherd.normalization-scans'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
780 #else
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
781 #set $wfdict['ptmshepherd.normalization-psms'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
782 #set $wfdict['ptmshepherd.normalization-scans'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
783 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
784 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
785 #if $cxt.varmod_masses != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
786 #set $wfdict['ptmshepherd.varmod_masses'] = $cxt.varmod_masses
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
787 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
788 #set $cxt = $prfx.ptm_annotation
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
789 #if $cxt.annotation_tol != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
790 #set $wfdict['ptmshepherd.annotation_tol'] = $cxt.annotation_tol
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
791 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
792 #if $cxt.annotation.annotation_source == 'unimod'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
793 #set $wfdict['ptmshepherd.annotation-unimod'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
794 #set $wfdict['ptmshepherd.annotation-common'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
795 #set $wfdict['ptmshepherd.annotation-glyco'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
796 #set $wfdict['ptmshepherd.annotation-custom'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
797 #elif $cxt.annotation.annotation_source == 'common'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
798 #set $wfdict['ptmshepherd.annotation-unimod'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
799 #set $wfdict['ptmshepherd.annotation-common'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
800 #set $wfdict['ptmshepherd.annotation-glyco'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
801 #set $wfdict['ptmshepherd.annotation-custom'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
802 #elif $cxt.annotation.annotation_source == 'glyco'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
803 #set $wfdict['ptmshepherd.annotation-unimod'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
804 #set $wfdict['ptmshepherd.annotation-common'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
805 #set $wfdict['ptmshepherd.annotation-glyco'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
806 #set $wfdict['ptmshepherd.annotation-custom'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
807 #elif $cxt.annotation.annotation_source == 'custom'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
808 #set $wfdict['ptmshepherd.annotation-unimod'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
809 #set $wfdict['ptmshepherd.annotation-common'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
810 #set $wfdict['ptmshepherd.annotation-glyco'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
811 #set $wfdict['ptmshepherd.annotation-custom'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
812 #set $wfdict['ptmshepherd.annotation_file'] = $cxt.annotation.annotation_file
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
813 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
814 #set $cxt = $prfx.ptm_localization
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
815 #if $cxt.nions is not None
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
816 #set $wfdict['ptmshepherd.iontype_a'] = str('a' in $cxt.nions).lower()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
817 #set $wfdict['ptmshepherd.iontype_b'] = str('b' in $cxt.nions).lower()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
818 #set $wfdict['ptmshepherd.iontype_c'] = str('c' in $cxt.nions).lower()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
819 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
820 #if $cxt.cions is not None
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
821 #set $wfdict['ptmshepherd.iontype_x'] = str('x' in $cxt.cions).lower()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
822 #set $wfdict['ptmshepherd.iontype_y'] = str('y' in $cxt.cions).lower()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
823 #set $wfdict['ptmshepherd.iontype_z'] = str('z' in $cxt.cions).lower()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
824 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
825 #if $cxt.spectra_maxfragcharge != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
826 #set $wfdict['ptmshepherd.spectra_maxfragcharge'] = $cxt.spectra_maxfragcharge
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
827 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
828 #set $wfdict['ptmshepherd.localization_allowed_res'] = $cxt.localization_allowed_res
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
829 #else
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
830 #set $wfdict['ptmshepherd.run-shepherd'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
831 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
832 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
833
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
834 <token name="@RE_EXCLUDEMOD@">@RE_AA@,@RE_FLOAT@</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
835 <token name="@RE_EXCLUDEMODS@">@RE_EXCLUDEMOD@(;\s*@RE_EXCLUDEMOD@)*</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
836
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
837 <!-- Label-free quantification options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
838 <xml name="label_free_quantification" token_expand="false">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
839 <section name="quant_ms1" expanded="@EXPAND@" title="Quant (MS1)">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
840 <conditional name="label_free_quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
841 <param name="label_free_quantification_run" type="select" label="Perform Label-Free Quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
842 <option value="default" selected="true">Use workflow default</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
843 <option value="no">No Label-Free Quantification</option>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
844 <option value="ionquant">Run IonQuant</option>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
845 <option value="freequant">Run FreeQuant</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
846 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
847 <when value="default"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
848 <when value="no"/>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
849 <when value="ionquant">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
850 <section name="ionquant" expanded="false" title="IonQuant Label-Free Quantification">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
851 <param name="mbr_select" type="select" optional="true" label="Match between runs (MBR)" help="ionquant.mbr">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
852 <option value="0">No</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
853 <option value="1">Yes</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
854 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
855 <param name="normalization" type="select" optional="true" label="Normalize" help="ionquant.normalization">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
856 <option value="0">No</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
857 <option value="1">Yes</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
858 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
859 <section name="feature_detection" expanded="false" title="Feature detection">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
860 <param name="mztol" type="integer" value="" optional="true" label="m/z tolerance in ppm" help="ionquant.mztol (default 10)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
861 <param name="rttol" type="float" value="" optional="true" label="RT tolerance (minutes)" help="ionquant.rttol (default 0.4)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
862 <param name="imtol" type="float" value="" optional="true" label="IM tolerance (1/k0)" help="ionquant.imtol (default 0.05)"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
863 </section>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
864 <section name="mbr" expanded="false" title="Match between runs (MBR)">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
865 <param name="mbrrttol" type="float" value="" optional="true" label="MBR RT tolerance (minutes)" help="ionquant.mbrrttol"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
866 <param name="mbrimtol" type="float" value="" optional="true" label="MBR IM tolerance (1/k0)" help="ionquant.mbrimtol"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
867 <param name="mbrmincorr" type="float" value="" optional="true" label="MBR min correlation" help="ionquant.mbrmincorr"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
868 <param name="mbrtoprun" type="integer" value="" optional="true" label="MBR top runs" help="ionquant.mbrtoprun"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
869 <param name="ionfdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR ion FDR" help="ionquant.ionfdr"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
870 <param name="peptidefdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR peptide FDR" help="ionquant.peptidefdr"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
871 <param name="proteinfdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR protein FDR" help="ionquant.proteinfdr"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
872 </section>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
873 <section name="topn" expanded="false" title="Top-N options">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
874 <param name="tp" type="integer" value="" min="0" optional="true" label="Top N ions" help="ionquant.tp"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
875 <param name="minfreq" type="float" value="" min="0.0" max="1.0" optional="true" label="Min freq" help="ionquant.minfreq"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
876 </section>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
877 <conditional name="labeling_conditional">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
878 <param name="labeling_option" type="select" label="Labeling option">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
879 <option value="lfq" selected="true">LFQ</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
880 <option value="labeling">Labeling</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
881 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
882 <when value="lfq">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
883 <section name="lfq" expanded="false" title="LFQ">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
884 <param name="maxlfq" type="select" optional="true" label="MaxLFQ" help="ionquant.maxlfq">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
885 <option value="0">No</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
886 <option value="1">Yes</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
887 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
888 <param name="minions" type="integer" value="" optional="true" label="Min ions" help="ionquant.minions"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
889 </section>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
890 </when>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
891 <when value="labeling">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
892 <section name="labeling" expanded="false" title="Labeling-based quant">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
893 <param name="light" type="select" label="Light" help="ionquant.light">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
894 <option value="" selected="true">none</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
895 <option value="C463.2366">C463.2366</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
896 <option value="C464.28596">C464.28596</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
897 <option value="C561.3387">C561.3387</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
898 <option value="K0;R0">K0;R0</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
899 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
900 <param name="medium" type="select" label="Medium" help="ionquant.medium">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
901 <option value="" selected="true">none</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
902 <option value="K4.025107;R6.020129">K4.025107;R6.020129</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
903 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
904 <param name="heavy" type="select" label="Heavy" help="ionquant.heavy">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
905 <option value="" selected="true">none</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
906 <option value="C467.2529">C467.2529</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
907 <option value="C470.29977">C470.29977</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
908 <option value="C567.3462">C567.3462</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
909 <option value="K8.014199;R10.008269">K8.014199;R10.008269</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
910 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
911 <param name="requantify" type="select" label="Re-quantify" help="ionquant.requantify">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
912 <option value="0">No</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
913 <option value="1" selected="true">Yes</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
914 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
915 </section>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
916 </when>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
917 </conditional>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
918 <section name="advanced" expanded="false" title="Advanced options">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
919 <param name="excludemods" type="text" optional="true" label="excludemods" help="ionquant.excludemods">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
920 <validator type="regex">^\s*@RE_EXCLUDEMODS@\s*$</validator>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
921 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
922 <param name="minscans" type="integer" value="" min="0" optional="true" label="Min scans" help="ionquant.minscans"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
923 <param name="minisotopes" type="integer" value="" min="1" max="3" optional="true" label="Min isotopes" help="ionquant.minisotopes"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
924 <param name="locprob" type="float" value="" min="0.0" max="1.0" optional="true" label="Min site probability" help="ionquant.locprob"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
925 <param name="writeindex" type="select" optional="true" label="Write index" help="ionquant.writeindex">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
926 <option value="0">No</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
927 <option value="1">Yes</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
928 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
929 </section>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
930 </section>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
931 </when>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
932 <when value="freequant">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
933 <section name="freequant" expanded="false" title="IonQuant Label-Free Quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
934 <param name="rt_tol" type="float" value="" min="0" optional="true" label="RT Window (minutes)"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
935 <param name="mz_tol" type="integer" value="" min="1" optional="true" label="m/z Window (ppm)"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
936 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
937 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
938 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
939 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
940 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
941
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
942 <!-- Set label-free quantification workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
943 <token name="@LABEL_FREE_QUANTIFICATION@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
944 #set $prfx = $wf.quant_ms1.label_free_quantification
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
945 #if $prfx.label_free_quantification_run == 'no'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
946 #set $wfdict['quantitation.run-label-free-quant'] = 'false'
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
947 #set $wfdict['ionquant.run-ionquant'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
948 #set $wfdict['freequant.run-freequant'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
949 #elif $prfx.label_free_quantification_run == 'ionquant'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
950 #set $wfdict['quantitation.run-label-free-quant'] = 'true'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
951 #set $wfdict['ionquant.run-ionquant'] = 'true'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
952 #set $wfdict['freequant.run-freequant'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
953 #set $cxt = $prfx.ionquant
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
954 #if $cxt.mbr_select != 'None'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
955 #set $wfdict['ionquant.mbr'] = $cxt.mbr_select
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
956 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
957 #if $cxt.normalization != 'None'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
958 #set $wfdict['ionquant.normalization'] = $cxt.normalization
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
959 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
960 #set $cxt = $prfx.ionquant.feature_detection
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
961 #if $cxt.mztol != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
962 #set $wfdict['ionquant.mztol'] = $cxt.mztol
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
963 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
964 #if $cxt.rttol != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
965 #set $wfdict['ionquant.rttol'] = $cxt.rttol
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
966 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
967 #if $cxt.imtol != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
968 #set $wfdict['ionquant.imtol'] = $cxt.imtol
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
969 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
970 #set $cxt = $prfx.ionquant.mbr
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
971 #if $cxt.mbrrttol != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
972 #set $wfdict['ionquant.mbrrttol'] = $cxt.mbrrttol
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
973 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
974 #if $cxt.mbrimtol != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
975 #set $wfdict['ionquant.mbrimtol'] = $cxt.mbrimtol
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
976 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
977 #if $cxt.mbrmincorr != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
978 #set $wfdict['ionquant.mbrmincorr'] = $cxt.mbrmincorr
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
979 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
980 #if $cxt.mbrtoprun != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
981 #set $wfdict['ionquant.mbrtoprun'] = $cxt.mbrtoprun
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
982 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
983 #if $cxt.ionfdr != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
984 #set $wfdict['ionquant.ionfdr'] = $cxt.ionfdr
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
985 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
986 #if $cxt.peptidefdr != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
987 #set $wfdict['ionquant.peptidefdr'] = $cxt.peptidefdr
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
988 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
989 #if $cxt.proteinfdr != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
990 #set $wfdict['ionquant.proteinfdr'] = $cxt.proteinfdr
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
991 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
992 #set $cxt = $prfx.ionquant.topn
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
993 #if $cxt.tp != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
994 #set $wfdict['ionquant.tp'] = $cxt.tp
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
995 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
996 #if $cxt.minfreq != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
997 #set $wfdict['ionquant.minfreq'] = $cxt.minfreq
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
998 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
999 #set $cxt = $prfx.ionquant.labeling_conditional
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1000 #if $cxt.labeling_option == 'labeling'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1001 #set $cxt = $prfx.ionquant.labeling_conditional.labeling
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1002 #set $wfdict['ionquant.use-labeling'] = 'true'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1003 #set $wfdict['ionquant.use-lfq'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1004 #set $wfdict['ionquant.light'] = $cxt.light
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1005 #set $wfdict['ionquant.medium'] = $cxt.medium
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1006 #set $wfdict['ionquant.heavy'] = $cxt.heavy
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1007 #set $wfdict['ionquant.requantify'] = $cxt.requantify
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1008 #else
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1009 #set $cxt = $prfx.ionquant.labeling_conditional.lfq
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1010 #set $wfdict['ionquant.use-labeling'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1011 #set $wfdict['ionquant.use-lfq'] = 'true'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1012 #if $cxt.maxlfq != 'None'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1013 #set $wfdict['ionquant.maxlfq'] = $cxt.maxlfq
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1014 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1015 #if $cxt.minions != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1016 #set $wfdict['ionquant.minions'] = $cxt.minions
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1017 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1018 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1019 #set $cxt = $prfx.ionquant.advanced
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1020 #if $cxt.excludemods != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1021 #set $wfdict['ionquant.excludemods'] = $cxt.excludemods
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1022 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1023 #if $cxt.minscans != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1024 #set $wfdict['ionquant.minscans'] = $cxt.minscans
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1025 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1026 #if $cxt.minisotopes != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1027 #set $wfdict['ionquant.minisotopes'] = $cxt.minisotopes
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1028 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1029 #if $cxt.locprob != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1030 #set $wfdict['ionquant.locprob'] = $cxt.locprob
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1031 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1032 #if $cxt.writeindex != 'None'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1033 #set $wfdict['ionquant.writeindex'] = $cxt.writeindex
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1034 #end if
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1035 #elif $prfx.label_free_quantification_run == 'freequant'
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1036 #set $wfdict['quantitation.run-label-free-quant'] = 'true'
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1037 #set $wfdict['ionquant.run-ionquant'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1038 #set $wfdict['freequant.run-freequant'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1039 #set $cxt = $prfx.freequant
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1040 #if $cxt.rt_tol != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1041 #set $wfdict['freequant.rt-tol'] = $cxt.rt_tol
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1042 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1043 #if $cxt.mz_tol != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1044 #set $wfdict['freequant.mz-tol'] = $cxt.mz_tol
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1045 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1046 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1047 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1048
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1049 <!--
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1050 Isobaric quantification options
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1051
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1052 TMT-n uses the following n first labels from TMT-18
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1053 TMT-18 "126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N, 134C, 135N"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1054 iTRAQ-4 "114, 115, 116, 117"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1055 iTRAQ-8 "113, 114, 115, 116, 117, 118, 119, 121"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1056 -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1057 <xml name="isobaric_quantification" token_expand="false" token_yes="true" token_no="false" token_plex="" token_level="2" token_virtual="false" token_pool="false" token_bridge="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1058 <section name="quant_iso" expanded="@EXPAND@" title="Quant (Isobaric)">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1059 <conditional name="isobaric_quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1060 <param name="isobaric_quantification_step" type="select" label="Perform Isobaric Quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1061 <option value="default">Use workflow defaults</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1062 <option value="yes" selected="@YES@">yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1063 <option value="no" selected="@NO@">no</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1064 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1065 <when value="default"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1066 <when value="no"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1067 <when value="yes">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1068 <section name="options" expanded="true" title="Isobaric Quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1069 <param name="quant_level" type="integer" value="@LEVEL@" min="1" max="3" label="MS level for the quantification"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1070 <param name="channel_num" type="text" value="@PLEX@" optional="true" label="Number of channels">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1071 <validator type="regex" message="">^TMT-\d?</validator>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1072 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1073 <param name="ref_tag" type="select" label="Set Unique tag to identify reference channels">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1074 <help>Virtual or specify a Reference sample tag: pool or Bridge</help>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1075 <option value="Virtual" selected="@VIRTUAL@">Virtual - Add an artificial reference channel</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1076 <option value="pool" selected="@POOL@">pool</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1077 <option value="Bridge" selected="@BRIDGE@">Bridge</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1078 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1079 <param name="groupby" type="select" optional="true" label="Group by level of summarization">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1080 <option value="0">Gene level</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1081 <option value="1">Protein</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1082 <option value="2">Peptide sequence</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1083 <option value="3">Multiple PTM sites</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1084 <option value="4">Single PTM site</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1085 <option value="-1">All</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1086 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1087 <param name="log2transformed" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Log2 transform the intensity"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1088 <param name="prot_norm" type="select" optional="true" label="normalization">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1089 <option value="0">None</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1090 <option value="1">MC (median centering)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1091 <option value="2">GN (median centering + variance scaling)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1092 <option value="-1">generate reports with all normalization options</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1093 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1094 <conditional name="glycan_conditional">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1095 <param name="use_glycan_composition" type="select" label="Perform Isobaric Quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1096 <option value="default">Use workflow defaults</option>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1097 <option value="no">no</option>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1098 <option value="yes">yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1099 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1100 <when value="default"/>
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1101 <when value="no"/>
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1102 <when value="yes">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1103 <param name="mod_tag" type="select" optional="true" label="PTM Mod tag">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1104 <option value="none">none</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1105 <option value="N-glyco">N-glyco</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1106 <option value="C(239.1629)">C(239.1629)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1107 <option value="K(-187.1524)">K(-187.1524)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1108 <option value="K(-262.1966)">K(-262.1966)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1109 <option value="K(114.0429),K(-115.12)">K(114.0429),K(-115.12)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1110 <option value="S(79.9663),T(79.9663),Y(79.9663)">S(79.9663),T(79.9663),Y(79.9663)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1111 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1112 <param name="min_site_prob" type="float" min="-1.0" max="1.0" optional="true" label="Minimum site probability">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1113 <help>site localization confidence thresholdr: -1 for global, 0 for search engine determined, above 0 for probability</help>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1114 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1115 <param name="glyco_qval" type="integer" value="-1" optional="true" label="Glycan FDR filter"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1116 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1117 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1118 <param name="unique_gene" type="select" optional="true" label="Peptide-Gene uniqueness">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1119 <option value="0">0: allow all PSMs</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1120 <option value="1">1: remove PSMs mapping to more than one GENE with evidence of expression in the dataset</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1121 <option value="2">2: remove all PSMs mapping to more than one GENE in the fasta file</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1122 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1123 <param name="unique_pep" type="select" optional="true" label="Peptide-Protein uniqueness">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1124 <option value="false">unique plus razor peptides</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1125 <option value="true">allow PSMs with unique peptides only</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1126 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1127 <param name="min_pep_prob" type="float" min="0" max="1.0" optional="true" label="only use PSMs with a minimum probability score"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1128 help="minimum PSM probability threshold (in addition to FDR-based filtering by Philosopher)"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1129 <param name="min_purity" type="float" min="0" max="1.0" optional="true" label="ion purity threshold (default 0.5)"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1130 <param name="min_percent" type="float" min="0" max="1.0" optional="true" label="ignore the lower % PSMs based on their summed abundances"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1131 help="e.g. value of 0.05 indicates removal of PSMs with the summed TMT reporter ions intensity in the lowest 5% of all PSMs"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1132 <param name="max_pep_prob_thres" type="float" min="0" max="1.0" optional="true" label="threshold for maximum peptide probability"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1133 <param name="min_ntt" type="integer" min="0" max="2" optional="true" label="minimum allowed number of enzymatic termini"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1134 <param name="aggregation_method" type="select" optional="true" label="the aggregation method from the PSM level to the specified level">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1135 <option value="0">0: median</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1136 <option value="1">1: weighted-ratio</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1137 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1138 <param name="prot_exclude" type="text" optional="true" label="Exclude proteins with specified tags at the beginning of the accession number"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1139 help="e.g. none: no exclusion; sp|,tr| : exclude protein with sp| or tr|">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1140 <validator type="regex">^(none|[a-zA-Z]+\|)$</validator>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1141 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1142 <param name="best_psm" type="select" optional="true" label="keep the best PSM only (highest summed TMT intensity) among all redundant PSMs within the same LC-MS run">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1143 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1144 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1145 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1146 <param name="psm_norm" type="select" optional="true" label="perform additional retention time-based normalization at the PSM level">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1147 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1148 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1149 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1150 <param name="allow_overlabel" type="select" optional="true" label="allow PSMs with TMT on S (when overlabeling on S was allowed in the database search)">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1151 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1152 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1153 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1154 <param name="allow_unlabeled" type="select" optional="true" label="allow PSMs without TMT tag or acetylation on the peptide n-terminus">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1155 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1156 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1157 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1158 <param name="outlier_removal" type="select" optional="true" label="perform outlier removal">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1159 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1160 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1161 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1162 <param name="ms1_int" type="select" optional="true" label="MS1 precursor ion intensity for reference sample abundance estimation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1163 <option value="true">Yes - use MS1 precursor ion intensity</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1164 <option value="false">No - use MS2 reference intensity</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1165 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1166 <param name="tolerance" type="integer" optional="true" label="Tolerance"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1167 <param name="top3_pep" type="select" optional="true" label="use top 3 most intense peptide ions as part of the reference sample abundance estimation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1168 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1169 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1170 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1171 <param name="print_RefInt" type="select" optional="true" label="print individual reference sample abundance estimates for each multiplex in the final reports">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1172 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1173 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1174 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1175 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1176 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1177 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1178 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1179 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1180
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1181 <!-- Set isobaric quantification workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1182 <token name="@ISOBARIC_QUANTIFICATION@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1183 #set $prfx = $wf.quant_iso.isobaric_quantification
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1184 #if $prfx.isobaric_quantification_step == 'no'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1185 #set $wfdict['tmtintegrator.run-tmtintegrator'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1186 #elif $prfx.isobaric_quantification_step == 'yes'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1187 #set $wfdict['tmtintegrator.run-tmtintegrator'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1188 #set $cxt = $prfx.options
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1189 #set $wfdict['tmtintegrator.quant_level'] = $cxt.quant_level
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1190 #set $wfdict['tmtintegrator.channel_num'] = $cxt.channel_num
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1191 #if $cxt.ref_tag == 'Virtual'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1192 #set $wfdict['tmtintegrator.add_Ref'] = -1
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1193 #else
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1194 #set $wfdict['tmtintegrator.add_Ref'] = 1
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1195 #set $wfdict['tmtintegrator.ref_tag'] = $cxt.ref_tag
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1196 #end if
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1197 #if $cxt.groupby != 'None'
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1198 #set $wfdict['tmtintegrator.groupby'] = $cxt.groupby
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1199 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1200 #set $wfdict['tmtintegrator.log2transformed'] = $cxt.log2transformed
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1201 #if $cxt.prot_norm != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1202 #set $wfdict['tmtintegrator.prot_norm'] = $cxt.prot_norm
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1203 #end if
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1204 #if $cxt.glycan_conditional.use_glycan_composition == 'no'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1205 #set $wfdict['tmtintegrator.use_glycan_composition'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1206 #elif $cxt.glycan_conditional.use_glycan_composition == 'yes'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1207 #set $wfdict['tmtintegrator.use_glycan_composition'] = 'true'
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1208 #if $cxt.glycan_conditional.mod_tag != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1209 #set $wfdict['tmtintegrator.mod_tag'] = $cxt.glycan_conditional.mod_tag
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1210 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1211 #if $cxt.glycan_conditional.min_site_prob != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1212 #set $wfdict['tmtintegrator.min_site_prob'] = $cxt.glycan_conditional.min_site_prob
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1213 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1214 #if $cxt.glycan_conditional.glyco_qval != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1215 #set $wfdict['tmtintegrator.glyco_qval'] = $cxt.glycan_conditional.glyco_qval
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1216 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1217 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1218 #if $cxt.unique_gene != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1219 #set $wfdict['tmtintegrator.unique_gene'] = $cxt.unique_gene
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1220 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1221 #if $cxt.unique_pep != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1222 #set $wfdict['tmtintegrator.unique_pep'] = $cxt.unique_pep
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1223 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1224 #if $cxt.min_pep_prob != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1225 #set $wfdict['tmtintegrator.min_pep_prob'] = $cxt.min_pep_prob
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1226 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1227 #if $cxt.min_purity != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1228 #set $wfdict['tmtintegrator.min_purity'] = $cxt.min_purity
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1229 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1230 #if $cxt.min_percent != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1231 #set $wfdict['tmtintegrator.min_percent'] = $cxt.min_percent
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1232 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1233 #if $cxt.max_pep_prob_thres != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1234 #set $wfdict['tmtintegrator.max_pep_prob_thres'] = $cxt.max_pep_prob_thres
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1235 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1236 #if $cxt.min_ntt != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1237 #set $wfdict['tmtintegrator.min_ntt'] = $cxt.min_ntt
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1238 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1239 #if $cxt.aggregation_method != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1240 #set $wfdict['tmtintegrator.aggregation_method'] = $cxt.aggregation_method
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1241 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1242 #if $cxt.prot_exclude != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1243 #set $wfdict['tmtintegrator.prot_exclude'] = $cxt.prot_exclude
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1244 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1245 #if $cxt.best_psm != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1246 #set $wfdict['tmtintegrator.best_psm'] = $cxt.best_psm
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1247 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1248 #if $cxt.psm_norm != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1249 #set $wfdict['tmtintegrator.psm_norm'] = $cxt.psm_norm
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1250 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1251 #if $cxt.allow_overlabel != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1252 #set $wfdict['tmtintegrator.allow_overlabel'] = $cxt.allow_overlabel
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1253 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1254 #if $cxt.allow_unlabeled != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1255 #set $wfdict['tmtintegrator.allow_unlabeled'] = $cxt.allow_unlabeled
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1256 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1257 #if $cxt.outlier_removal != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1258 #set $wfdict['tmtintegrator.outlier_removal'] = $cxt.outlier_removal
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1259 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1260 #if $cxt.ms1_int != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1261 #set $wfdict['tmtintegrator.ms1_int'] = $cxt.ms1_int
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1262 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1263 #if $cxt.tolerance != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1264 #set $wfdict['tmtintegrator.tolerance'] = $cxt.tolerance
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1265 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1266 #if $cxt.top3_pep != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1267 #set $wfdict['tmtintegrator.top3_pep'] = $cxt.top3_pep
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1268 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1269 #if $cxt.print_RefInt != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1270 #set $wfdict['tmtintegrator.print_RefInt'] = $cxt.print_RefInt
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1271 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1272 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1273 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1274
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1275 <xml name="dia_pseuedo_ms2" token_expand="false" token_yes="false" token_no="true">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1276 <section name="dia_pseudo" expanded="@EXPAND@" title="DIA Pseudo MS2">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1277 <conditional name="diatracer">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1278 <param name="diatracer_step" type="select" label="Run diaTracer">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1279 <option value="default">Use workflow defaults</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1280 <option value="yes" selected="@YES@">yes</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1281 <option value="no" selected="@NO@">no</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1282 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1283 <when value="default"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1284 <when value="no"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1285 <when value="yes">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1286 <section name="options" expanded="true" title="diaPASEF Spectrum Deconvolution">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1287 <param name="corr_threshold" type="float" value="0.3" label="Corr Threshold"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1288 <param name="delta_apex_im" type="float" value="0.01" label="Delta Apex IM"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1289 <param name="delta_apex_rt" type="integer" value="3" label="Delta Apex RT"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1290 <param name="rf_max" type="integer" value="500" label="RF max" />
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1291 <param name="mass_defect_offset" type="float" value="0.1" label="Mass Defect Offset"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1292 <param name="mass_defect_filter" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Mass Defect Filter"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1293 </section>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1294 </when>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1295 </conditional>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1296 </section>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1297 </xml>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1298 <token name="@DIA_PSEUDO_MS2@"><![CDATA[
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1299 #set $prfx = $wf.dia_pseudo.diatracer
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1300 #if $prfx.diatracer_step == 'no'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1301 #set $wfdict['diatracer.run-diatracer'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1302 #elif $prfx.diatracer_step == 'yes'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1303 #set $wfdict['diatracer.run-diatracer'] = 'true'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1304 #set $cxt = $prfx.options
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1305 #set $wfdict['diatracer.corr-threshold'] = $cxt.corr_threshold
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1306 #set $wfdict['diatracer.delta-apex-im'] = $cxt.delta_apex_im
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1307 #set $wfdict['diatracer.delta-apex-rt'] = $cxt.delta_apex_rt
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1308 #set $wfdict['diatracer.rf-max'] = $cxt.rf_max
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1309 #set $wfdict['diatracer.mass-defect-offset'] = $cxt.mass_defect_offset
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1310 #set $wfdict['diatracer.mass-defect-filter'] = $cxt.mass_defect_filter
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1311 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1312 ]]></token>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1313
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1314 <xml name="diann_quantification" token_expand="false" token_yes="true" token_no="false">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1315 <section name="quant_dia" expanded="@EXPAND@" title="Quant (DIA)">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1316 <conditional name="diann_quantification">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1317 <param name="diann_quantification_step" type="select" label="Perform DIA Quantification with DIA-NN">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1318 <option value="default">Use workflow defaults</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1319 <option value="yes" selected="@YES@">yes</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1320 <option value="no" selected="@NO@">no</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1321 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1322 <when value="default"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1323 <when value="no"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1324 <when value="yes">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1325 <section name="options" expanded="true" title="Isobaric Quantification">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1326 <param name="qvalue" type="float" value="0.01" min="0.0" max="1.0" optional="true" label="Precursor FDR" help="default 0.01"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1327 <param name="generate_msstats" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Generate MSStats input"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1328 <param name="unrelated_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Unrelated runs"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1329 <param name="use_predicted_spectra" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Replace library spectra with predicted"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1330 <param name="library" type="data" format="csv,tsv,xls,txt,binary" optional="true" label="Spectral Library"/>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1331 <param name="quantification_strategy" type="select" optional="true" label="Quantification strategy" help="default: Robust LC (high precision)">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1332 <option value="0">Any LC (high accuracy)</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1333 <option value="1">Any LC (high precision)</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1334 <option value="2">Robust LC (high accuracy)</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1335 <option value="3">Robust LC (high precision)</option>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1336 </param>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1337 </section>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1338 </when>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1339 </conditional>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1340 </section>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1341 </xml>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1342 <token name="@DIANN_QUANTIFICATION@"><![CDATA[
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1343 #set $prfx = $wf.quant_dia.diann_quantification
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1344 #if $prfx.diann_quantification_step == 'no'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1345 #set $wfdict['diann.run-dia-nn'] = 'false'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1346 #elif $prfx.diann_quantification_step == 'yes'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1347 #set $wfdict['diann.run-dia-nn'] = 'true'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1348 #set $cxt = $prfx.options
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1349 #if $cxt.qvalue != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1350 #set $wfdict['diann.q-value'] = $cxt.qvalue
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1351 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1352 #set $wfdict['diann.generate-msstats'] = $cxt.generate_msstats
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1353 #set $wfdict['diann.unrelated-runs'] = $cxt.unrelated_runs
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1354 #set $wfdict['diann.use-predicted-spectra'] = $cxt.use_predicted_spectra
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1355 #if $cxt.quantification_strategy != ''
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1356 #set $wfdict['diann.quantification-strategy'] = $cxt.quantification_strategy
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1357 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1358 #if $cxt.library
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1359 ln -s '$cxt.library' './diann_lib.speclib'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1360 #set $wfdict['diann.library'] = 'diann_lib.speclib'
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1361 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1362 #end if
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1363 ]]></token>
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1364
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1365
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1366
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1367 <!-- License agreement texts. -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1368 <token name="@MSFRAGGER_LICENSE_AGREEMENT@">
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1369 MSFragger is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: http://msfragger-upgrader.nesvilab.org/upgrader/LICENSE-ACADEMIC.pdf. This license provides with non-exclusive, non-transferable right to use MSFragger solely for academic research, non-commercial or educational purposes. I agree to be subject to the terms and conditions of this license. I understand that to use MSFragger for other purposes requires a commercial license from the University of Michigan Office of Tech Transfer.
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1370 </token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1371 <token name="@IONQUANT_LICENSE_AGREEMENT@">
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1372 IonQuant is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: https://msfragger-upgrader.nesvilab.org/ionquant/LICENSE-ACADEMIC.pdf
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1373 </token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1374 <token name="@THERMO_RAW_READER_LICENSE_AGREEMENT@">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1375 I agree to the terms of Thermo (c) Raw File Reader License Agreement: http://msfragger-upgrader.nesvilab.org/upgrader/RawFileRdr_License_Agreement_RevA.pdf
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1376 </token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1377 <token name="@BRUKER_LICENSE_AGREEMENT@">
7
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
galaxyp
parents: 6
diff changeset
1378 I agree to the terms of Bruker SDK library distribution conditions: http://msfragger-upgrader.nesvilab.org/upgrader/EULA%20TDF-SDK.pdf
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1379 </token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1380 <token name="@LICENSE_AGREEMENTS@">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1381 @MSFRAGGER_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1382 @IONQUANT_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1383 @THERMO_RAW_READER_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1384 @BRUKER_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1385 </token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1386
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1387 <!-- User must check box agreeing to MSFragger license agreement. -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1388 <xml name="license_agreements">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1389 <param name="license_agreements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="I understand that these tools, including MSFragger, IonQuant, Bruker, and Thermo Raw File Reader, are available freely for academic research and educational purposes only, and agree to the following terms.">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1390 <validator type="expression" message="You must agree to the MSFragger license!">value == True</validator>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1391 <help><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1392 @MSFRAGGER_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1393 <br/><br/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1394 @IONQUANT_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1395 <br/><br/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1396 @THERMO_RAW_READER_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1397 <br/><br/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1398 @BRUKER_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1399 ]]></help>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1400 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1401 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1402
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1403 <xml name="citations">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1404 <citations>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1405 <citation type="doi">10.1038/s41592-020-0912-y</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1406 <citation type="doi">10.1038/nmeth.4256</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1407 <citation type="doi">10.1038/s41467-020-17921-y</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1408 <citation type="doi">10.1038/s41592-020-0967-9</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1409 <citation type="doi">10.1021/acs.jproteome.0c00119</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1410 <citation type="doi">10.1074/mcp.TIR120.002216</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1411 <citation type="doi">10.1074/mcp.TIR120.002048</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1412 <citation type="doi">10.1016/j.mcpro.2021.100077</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1413 <citation type="doi">10.1021/acs.jproteome.0c00544</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1414 <citation type="doi">10.1038/nmeth.3255</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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1415 <yield />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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1416 </citations>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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1417 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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1418 </macros>