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annotate msgfplus.xml @ 0:dbc77b37e20f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
author galaxyp
date Fri, 06 Nov 2015 14:31:57 -0500
parents
children 08b316ae9ec4
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0
dbc77b37e20f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
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1 <tool id="msgfplus" name="MS-GF+" version="0.1">
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2 <description>
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3 Identifies peptides in tandem mass spectra using the MS-GF+ search engine.
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="10089">msgfplus</requirement>
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7 <environment_variable name="LC_ALL" action="set_to">C</environment_variable>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" description="Job Failed" />
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11 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
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12 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
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13 </stdio>
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14 <command>
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15 <![CDATA[
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16 #set $db_name = $d.display_name.replace(".fasta", "") + ".fasta"
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17 #set $input_name = $s.display_name
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18 #set $output_name = $input_name.replace(".mzML", "") + ".mzid"
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19 ln -s '$s' '${input_name}' &&
dbc77b37e20f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit e6dd776a0df16d06df3bd2f230ca80c7420d9125-dirty
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20 ln -s '$d' '${db_name}' &&
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21
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22 java -jar \$(which MSGFPlus.jar)
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23 -s '$input_name'
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24 -d '$db_name'
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25 -thread \${GALAXY_SLOTS:-1}
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26
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27 -tda $tda
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28 -t $t$precursor_ion_tol_units
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29 -ti $advanced.isotope_low,$advanced.isotope_high
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30 -m $advanced.m
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31 -inst $inst
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32 -e $e
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33 -protocol $advanced.protocol
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34 -ntt $ntt
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35 -minLength $advanced.minLength
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36 -maxLength $advanced.maxLength
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37 -minCharge $advanced.minCharge
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38 -maxCharge $advanced.maxCharge
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39 -n $advanced.n
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40 -addFeatures $advanced.addFeatures
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41 &&
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42 mv '$output_name' output
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43 ]]>
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44 </command>
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45 <inputs>
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46 <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/>
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47 <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/>
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48 <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" />
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49 <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/>
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50 <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments">
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51 <option value="ppm" selected="true">Parts per million (ppm)</option>
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52 <option value="Da">Daltons</option>
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53 </param>
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54 <param argument="-inst" label="Instrument type" type="select" help="The instrument type that generated the MS/MS spectra is used to determine the scoring model">
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55 <option value="0" selected="true">Low-res (LCQ/LTQ)</option>
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56 <option value="1" >High-res (LTQ-Orbitrap)</option>
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57 <option value="2" >Q-TOF</option>
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58 <option value="3" >Q-Exactive</option>
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59 </param>
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60 <param argument="-e" type="select" label="Enzyme" help="Enzyme used to digest proteins in sample preparation; trypsin is the most commonly used enzyme">
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61 <option value="0">Unspecific cleavage</option>
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62 <option value="1" selected="true">Trypsin, no P rule</option>
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63 <option value="2">Chymotrypsin, no P rule (FYWL)</option>
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64 <option value="3">Lys-C, no P rule</option>
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65 <option value="4">Lys-N</option>
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66 <option value="5">Glu-C (glutamyl endopeptidase)</option>
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67 <option value="6">Arg-C</option>
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68 <option value="7">Asp-N</option>
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69 <option value="8">Alpha-lytic protease</option>
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70 <option value="9">No enzyme</option>
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71 </param>
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72 <param argument="-ntt" type="select" format="text" label="Number of tolerable termini" help="Semi-specific requires more time than fully specific; non-specific requires much more.">
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73 <option value="2" selected="true">Fully specific (both termini match cleavage rules)</option>
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74 <option value="1">Semi-specific (at least one terminus must match cleavage rules)</option>
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75 <option value="0">Non-specific (neither terminus is required to match cleavage rules)</option>
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76 </param>
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77 <!--
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78 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
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79 <options from_file="searchgui_mods.loc">
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80 <column name="name" index="0" />
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81 <column name="value" index="0" />
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82 </options>
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83 </param>
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84 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
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85 <options from_file="searchgui_mods.loc">
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86 <column name="name" index="0" />
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87 <column name="value" index="0" />
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88 </options>
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89 </param>-->
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90
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91 <!-- MS-GF+ ADVANCED PARAMETERS -->
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92 <section name="advanced" title="Advanced Options">
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93 <param argument="-minCharge" label="Minimum precursor charge" value="2" type="integer" help="Minimum precursor charge to consider if charges are not specified in the spectrum file"/>
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94 <param argument="-maxCharge" label="Maximum precursor charge" value="3" type="integer" help="Maximum precursor charge to consider if charges are not specified in the spectrum file"/>
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95 <param argument="-minLength" label="Minimum peptide length" value="6" type="integer" help="Minimum peptide length to consider"/>
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96 <param argument="-maxLength" label="Maximum peptide length" value="40" type="integer" help="Maximum peptide length to consider"/>
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97 <param name="num_ptms" label="Maximum modifications allowed per peptide" type="integer" value="2" />
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98 <param argument="-m" label="Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
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99 <option value="0" selected="True">As written in the spectrum or CID if no info</option>
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100 <option value="1" >CID</option>
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101 <option value="2" >ETD</option>
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102 <option value="3" >HCD</option>
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103 </param>
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104 <param argument="-protocol" label="Protocol type" type="select" help="Protocols are used to enable scoring parameters for enriched and/or labeled samples">
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105 <option value="0" selected="True">Automatic</option>
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106 <option value="1" >Phosphorylation</option>
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107 <option value="2" >iTRAQ</option>
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108 <option value="3" >iTRAQPhospho</option>
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109 <option value="4" >TMT</option>
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110 <option value="5" >Standard</option>
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111 </param>
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112 <param argument="-n" label="Maximum matches per spectrum" type="integer" value="1" help="Number of peptide matches per spectrum to report" />
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113 <param argument="-addFeatures" label="Calculate additional scoring features?" type="boolean" truevalue="1" falsevalue="0" help="If true, several extra derivative scores are calculated for each match" />
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114 <param name="isotope_low" label="Lower isotope error range" type="integer" value="0" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation (-ti)" />
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115 <param name="isotope_high" label="Upper isotope error range" type="integer" value="1" />
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116 </section>
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117 </inputs>
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118 <outputs>
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119 <data name="output" format="mzid" from_work_dir="output" />
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120 </outputs>
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121 <tests>
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122 <test>
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123 <param name="s" value="input/201208-378803.mzML" />
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124 <param name="d" value="input/cow.protein.PRG2012-subset.fasta" />
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125 <output name="output" file="201208-378803-msgf.mzid" lines_diff="12" />
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126 </test>
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127 <test>
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128 <param name="s" value="input/201208-378803.mzML" />
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129 <param name="d" value="input/cow.protein.PRG2012-subset.fasta" />
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130 <param name="tda" value="1" />
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131 <param name="t" value="0.02" />
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132 <param name="precursor_ion_tol_units" value="Da" />
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133 <param name="isotope_low" value="-1" />
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134 <param name="isotope_high" value="0" />
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135 <param name="m" value="1" />
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136 <param name="inst" value="1" />
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137 <param name="e" value="3" />
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138 <param name="ntt" value="1" />
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139 <param name="protocol" value="2" />
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140 <param name="minLength" value="10" />
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141 <param name="maxLength" value="20" />
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142 <param name="minCharge" value="2" />
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143 <param name="maxCharge" value="6" />
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144 <param name="n" value="2" />
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145 <param name="addFeatures" value="1" />
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146 <output name="output" file="201208-378803-msgf-2mmu-semi-tryptic.mzid" lines_diff="12" />
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147 </test>
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148 </tests>
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149 <help>
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150 **What it does**
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151
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152 Performs protein identification via database search using MS-GF+.
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153
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154 </help>
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155 <citations>
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156 <citation type="doi">10.1038/ncomms6277</citation>
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157 <citation type="doi">10.1021/pr8001244</citation>
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158 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Gruening, B, Chambers, MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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159 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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160 </citations>
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161 </tool>