Mercurial > repos > galaxyp > meta_proteome_analyzer

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer commit 681518afc38787fd942ce201938c12c1dcdab1d1"
author galaxyp
date Sun, 03 Jan 2021 20:30:02 +0000
parents c587a54c70ad
children
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c587a54c70ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer commit 02be64dadeda429d0cf96806b7013820d087d8b9"
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1 <tool id="meta_proteome_analyzer" name="MetaProteomeAnalyzer" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>
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3 functional and taxonomic characterization of proteins
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4 </description>
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c587a54c70ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer commit 02be64dadeda429d0cf96806b7013820d087d8b9"
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5 <macros>
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6 <token name="@TOOL_VERSION@">2.0.0</token>
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7 <token name="@WRAPPER_VERSION@">1</token>
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8 <xml name="test_output" token_name="" token_has_text="">
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9 <output name="output_PSMs">
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10 <assert_contents>
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11 <has_text text="A2SPK1" />
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12 </assert_contents>
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13 <yield/>
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14 </output>
c587a54c70ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer commit 02be64dadeda429d0cf96806b7013820d087d8b9"
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15 </xml>
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16 </macros>
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17 <requirements>
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18 <requirement type="package" version="@TOOL_VERSION@">mpa-portable</requirement>
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19 </requirements>
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20 <stdio>
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21 <regex match="Could not allocate metaspace" source="both" level="fatal_oom" description="Insufficient memory" />
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22 <regex match="OutOfMemoryError" source="both" level="fatal_oom" description="Insufficient memory" />
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23
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24 </stdio>
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25 <command detect_errors="exit_code">
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26 <![CDATA[
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27 mkdir -p output_dir &&
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28 ## copy mpa conf dir to working dir
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29 jar_dir=`mpa-portable -get_jar_dir` &&
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30
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31 cp -R \$jar_dir/conf . &&
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32
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33 ## echo the search engines to run
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34 #set $search_engines = str($engines).split(',')
c587a54c70ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer commit 02be64dadeda429d0cf96806b7013820d087d8b9"
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35 echo "$engines" &&
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36 echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}" &&
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37
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38 #for $mgf in $peak_lists:
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39 #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
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40 ln -s -f '${mgf}' '${input_name}' &&
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41 #set $encoded_id = $__app__.security.encode_id($mgf.id)
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42 echo "Spectrums:${mgf.display_name}(API:${encoded_id}) " &&
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43 #end for
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44 cp "${input_database}" input_database.fasta &&
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45
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46 ######################
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47 ## MPA ##
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48 ######################
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49 mpa-portable de.mpa.cli.CmdLineInterface --exec_dir=exec_dir -Xmx2048m
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50 -spectrum_files "\$(pwd)"
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51 -database input_database.fasta
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52 -missed_cleav $missed_cleavages
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53 -prec_tol ${precursor_options.prec_tol}${precursor_options.prec_tol_units}
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54 -frag_tol ${precursor_options.frag_tol}Da
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55 -xtandem #if 'X!Tandem' in $search_engines then 1 else 0#
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56 -comet #if 'Comet' in $search_engines then 1 else 0#
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57 -msgf #if 'MSGF' in $search_engines then 1 else 0#
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58 -generate_metaproteins $generate_metaproteins
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59 -iterative_search $iterative_search
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60 -fragment_method $fragment_method
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61 -peptide_index $peptide_index
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62 -fdr_threshold $fdr_threshold
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63 -semi_tryptic $semi_tryptic
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64 -output_folder output_dir
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65 -threads "\${GALAXY_SLOTS:-12}" &&
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66 #if $generate_metaproteins == "1"
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67 mv ./output_dir/*_metaproteins.csv metaproteins.csv &&
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68 mv ./output_dir/*_metaprotein_taxa.csv metaprotein_taxa.csv &&
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69 #end if
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70 mv ./output_dir/*_peptides.csv peptides.csv &&
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71 mv ./output_dir/*_proteins.csv proteins.csv &&
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72 mv ./output_dir/*_psms.csv psms.csv &&
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73 mv ./output_dir/*_spectrum_ids.csv spectrum_ids.csv
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74 ]]>
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75 </command>
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76 <inputs>
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77 <param format="fasta" name="input_database" type="data" label="Protein Database"
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78 help="Select FASTA database from history"/>
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79 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
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80 help="Select appropriate MGF dataset(s) from history" />
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81 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
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82 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
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83 <section name="precursor_options" expanded="false" title="Precursor Options">
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84 <param name="prec_tol_units" type="select" label="Precursor Ion Tolerance Units"
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85 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
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86 <option value="ppm">Parts per million (ppm)</option>
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87 <option value="Da">Daltons</option>
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88 </param>
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89 <param name="prec_tol" type="float" value="10" label="Percursor Ion Tolerance"
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90 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
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91 <param name="frag_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"
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92 help="Provide error value for fragment ions, based on instrument used"/>
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93 </section>
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94 <!-- Search Engine Selection -->
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95 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
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96 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
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97 <option value="X!Tandem" selected="True">X!Tandem</option>
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98 <option value="MSGF">MS-GF+</option>
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99 <option value="Comet">Comet</option>
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100 </param>
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101 <param argument="-generate_metaproteins" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Meta-protein generation" help="aka. protein grouping"/>
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102 <param argument="-iterative_search" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Iterative searching" help="aka. two-step searching"/>
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103 <param argument="-semi_tryptic" type="boolean" truevalue="1" falsevalue="0" checked="false" label="" help="Semi-tryptic cleavage"/>
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104 <param argument="-fragment_method" type="select" label="Fragmentation method" help="for the MS instrument">
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105 <option value="1" selected="true">CID</option>
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106 <option value="2">HCD</option>
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107 <option value="3">ETD</option>
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108 </param>
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109 <param argument="-peptide_index" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Peptide indexing (of FASTA database)" help=""/>
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110 <param argument="-fdr_threshold" type="float" value="0.05" min="0" max="1" label="FDR threshold for filtering" help=""/>
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111 </inputs>
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112 <outputs>
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113 <data format="tabular" name="output_proteins" from_work_dir="proteins.csv" label="${tool.name} on ${on_string}: proteins">
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114 <actions>
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115 <action name="comment_lines" type="metadata" default="1" />
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116 <action name="column_names" type="metadata" default="Protein_No,Protein_Accession,Protein_Description,Protein_Taxonomy,Sequence_Coverage,Peptide_Count,NSAF,emPAI,Spectral_Count,Isoelectric_Point,Molecular_Weight,Protein_Sequence,Peptides" />
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117 </actions>
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118 </data>
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119 <data format="tabular" name="output_peptides" from_work_dir="peptides.csv" label="${tool.name} on ${on_string}: peptides">
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120 <actions>
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121 <action name="comment_lines" type="metadata" default="1" />
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122 <action name="column_names" type="metadata" default="Peptide_Num,Protein_Accessions,Peptide_Sequence,Protein_Count,Spectral_Count,Taxonomic_Group,Taxonomic_Rank,NCBI_Taxonomy_ID" />
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123 </actions>
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124 </data>
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125 <data format="tabular" name="output_PSMs" from_work_dir="psms.csv" label="${tool.name} on ${on_string}: PSMs">
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126 <actions>
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127 <action name="comment_lines" type="metadata" default="1" />
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128 <action name="column_names" type="metadata" default="PSM_Num,Protein_Accessions,Peptide_Sequence,Spectrum_Title,Charge,Search_Engine,q-value,Score" />
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129 </actions>
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130 </data>
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131 <data format="tabular" name="output_spectrum_ids" from_work_dir="spectrum_ids.csv" label="${tool.name} on ${on_string}: spectrum_ids">
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132 <actions>
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133 <action name="comment_lines" type="metadata" default="1" />
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134 <action name="column_names" type="metadata" default="Spectrum_Number,Spectrum_ID,Spectrum_Title,Peptides,Protein_Accessions" />
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135 </actions>
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136 </data>
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137 <data format="tabular" name="output_metaproteins" from_work_dir="metaproteins.csv" label="${tool.name} on ${on_string}: metaproteins">
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138 <filter>generate_metaproteins</filter>
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139 <actions>
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140 <action name="comment_lines" type="metadata" default="1" />
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141 <action name="column_names" type="metadata" default="Meta-Protein_Num,Meta-Protein_Accession,Meta-Protein_Description,Meta-Protein_Taxonomy,Meta-Protein_UniRef100,Meta-Protein_UniRef90,Meta-Protein_UniRef50,Meta-Protein_KO,Meta-Protein_EC,Peptide_Count,Spectral_Count,Proteins,Peptides" />
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142 </actions>
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143 </data>
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144 <data format="tabular" name="output_metaprotein_taxa" from_work_dir="metaprotein_taxa.csv" label="${tool.name} on ${on_string}: metaprotein_taxa">
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145 <filter>generate_metaproteins</filter>
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146 <actions>
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147 <action name="comment_lines" type="metadata" default="1" />
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148 <action name="column_names" type="metadata" default="Unclassified,Superkingdom,Kingdom,Phylum,Class,Order,Family,Genus,Species,Subspecies,Num_Peptides,Spectral_Count" />
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149 </actions>
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150 </data>
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151 </outputs>
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152 <tests>
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153 <test expect_num_outputs="6">
1
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154 <param name="peak_lists" value="Test416Ebendorf.mgf" ftype="mgf"/>
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155 <param name="input_database" value="searchdb.fa" ftype="fasta"/>
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156 <param name="missed_cleavages" value="2"/>
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157 <param name="prec_tol" value="ppm"/>
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158 <param name="prec_tol" value="10"/>
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159 <param name="frag_tol" value="0.5"/>
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160 <param name="engines" value="X!Tandem,MSGF,Comet"/>
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161 <expand macro="test_output" name="output_proteins" has_text="B8GJQ7"/>
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162 <expand macro="test_output" name="output_peptides" has_text="B8GJQ7"/>
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163 <expand macro="test_output" name="output_PSMs" has_text="B8GJQ7">
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164 <assert_contents>
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165 <has_text text="X!Tandem" />
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166 </assert_contents>
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167 </expand>
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168 <expand macro="test_output" name="output_spectrum_ids" has_text="B8GJQ7"/>
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169 <expand macro="test_output" name="output_metaproteins" has_text="B8GJQ7"/>
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170 <expand macro="test_output" name="output_metaprotein_taxa" has_text="Unknown Superkingdomq"/>
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171 </test>
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172 <test expect_num_outputs="4">
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173 <param name="peak_lists" value="Test416Ebendorf.mgf" ftype="mgf"/>
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174 <param name="input_database" value="searchdb.fa" ftype="fasta"/>
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175 <param name="missed_cleavages" value="2"/>
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176 <param name="prec_tol" value="ppm"/>
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177 <param name="prec_tol" value="10"/>
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178 <param name="frag_tol" value="0.5"/>
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179 <param name="engines" value="MSGF,Comet"/>
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180 <param name="generate_metaproteins" value="0"/>
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181 <expand macro="test_output" name="output_proteins" has_text="B8GJQ7"/>
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182 <expand macro="test_output" name="output_peptides" has_text="B8GJQ7"/>
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183 <expand macro="test_output" name="output_PSMs" has_text="B8GJQ7">
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184 <assert_contents>
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185 <not_has_text text="X!Tandem" />
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186 </assert_contents>
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187 </expand>
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188 <expand macro="test_output" name="output_spectrum_ids" has_text="B8GJQ7"/>
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189 <expand macro="test_output" name="output_metaproteins" has_text="B8GJQ7"/>
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190 <expand macro="test_output" name="output_metaprotein_taxa" has_text="Unknown Superkingdomq"/>
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191 </test>
0
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192 </tests>
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193 <help>
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194 **What it does**
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195
1
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196 =======
0
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197
1
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198 MetaProteomeAnalyzer (MPA) performs identification of proteins and in-depth analysis of metaproteomics (and also proteomics) data. The MPA software currently supports the database search engines Comet, MS-GF+ and X!Tandem taking MGF spectrum files as input data. User-provided FASTA databases (preferably downloaded from UniProtKB) are formatted automatically.
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199
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200 https://github.com/compomics/meta-proteome-analyzer
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201
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202 ----
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203
1
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204 Outputs
0
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205 =======
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206
1
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207 MPA generates 6 tabular outputs:
0
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208
1
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209 * psms
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210 * peptides
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211 * proteins
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212 * spectrum_ids
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213 * metaproteins
2
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214 * metaprotein_taxa
0
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215 </help>
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216 <citations>
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217 <citation type="doi">10.1021/pr501246w</citation>
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218 </citations>
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219 </tool>