Mercurial > repos > galaxyp > maxquant_mqpar

annotate maxquant_mqpar.xml @ 2:3fc2116ac6d9 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
author galaxyp
date Thu, 15 Aug 2019 08:09:38 -0400
parents 256cc0e17454
children 2d67fb758956
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256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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1 <tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <requirements>
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6 <requirement type="package" version="@VERSION@">maxquant</requirement>
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7 <requirement type="package" version="3.7">python</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #import re
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11
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12 python3 '$__tool_directory__/mqwrapper.py'
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13 --num_threads=\${GALAXY_SLOTS:-1}
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14 --substitution_rx='@SUBSTITUTION_RX@'
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15 #if $infile.select == "mzxml_files"
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16 --mzxml_files='$infile.mzxml_files'
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17 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $infile.mzxml_files])
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18 #else
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19 --raw_files='$infile.raw_files'
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20 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $infile.raw_files])
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21 #end if
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22 --infile_names='$names'
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23 --version='@VERSION@'
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24 --fasta_files='$fasta_files'
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25 --identifier_parse_rule='$identifier_parse_rule'
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26 --description_parse_rule='$description_parse_rule'
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27 --mqpar_in='$mqpar_in'
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28
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29 --evidence='$evidence'
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30 --msms='$msms'
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31 --parameters='$parameters'
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32 --peptides='$peptides'
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33 --proteinGroups='$proteinGroups'
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34 --allPeptides='$allPeptides'
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35 --libraryMatch='$libraryMatch'
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36 --matchedFeatures='$matchedFeatures'
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37 --modificationSpecificPeptides='$modificationSpecificPeptides'
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38 --ms3Scans='$ms3Scans'
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39 --msmsScans='$msmsScans'
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40 --mzRange='$mzRange'
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41 --peptideSection='$peptideSection'
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42 --summary='$summary'
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43 --mzTab='$mzTab'
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44 --output_all='$output_all'
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45 --mqpar_out='$mqpar_out'
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46
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47 > '$log'
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48 ]]></command>
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49 <inputs>
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50 <conditional name="infile">
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51 <param name="select" type="select" label="choose the type of your input files">
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52 <option value="raw_files">Thermo.raw</option>
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53 <option value="mzxml_files">mzXML</option>
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54 </param>
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55 <when value="raw_files">
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56 <param multiple="true" name="raw_files" type="data"
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57 format="thermo.raw" label="RAW Files"
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58 help="Specify one or more Thermo RAW files" />
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59 </when>
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60 <when value="mzxml_files">
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61 <param multiple="true" name="mzxml_files" type="data"
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62 format="mzxml" label="mzXML Files"
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63 help="Specify one or more mzXML files" />
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64 </when>
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65 </conditional>
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66 <param format="fasta" multiple="true" name="fasta_files"
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67 type="data" label="FASTA files"
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68 help="Specify one or more FASTA databases." />
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69 <param name="identifier_parse_rule" type="text"
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70 label="identifier parse rule" value="^&gt;.*\|(.*)\|.*$">
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71 <sanitizer>
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72 <valid initial="string.printable">
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73 <remove value="&apos;"/>
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74 </valid>
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75 </sanitizer>
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76 </param>
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77 <param name="description_parse_rule" type="text"
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78 label="description parse rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$"
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79 help="Modify parse rules if needed">
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80 <sanitizer>
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81 <valid initial="string.printable">
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82 <remove value="&apos;"/>
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83 </valid>
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84 </sanitizer>
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85 </param>
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86 <param type="data" name="mqpar_in" format="xml"
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87 label="mqpar.xml file with your search parameters. RAW file names
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88 must match the names displayed in galaxy. Their paths
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89 from the local machine are ignored. E.g. a file named
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90 'test01.raw' in galaxy can either be named 'test01.raw' or
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91 'D:\path\to\test01.raw' in the mqpar.xml."/>
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92
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93 <param type="select" name="output" label="Select the desired outputs."
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94 multiple="true" optional="false">
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95 <expand macro="output_option" name="proteinGroups" label="Protein Groups"/>
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96 <expand macro="output_option" name="mqpar_out" label="mqpar.xml"/>
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97 <expand macro="output_option" name="peptides" label="Peptides"/>
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98 <expand macro="output_option" name="evidence" label="Evidence"/>
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99 <expand macro="output_option" name="parameters" label="Tabular Paramters"/>
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100 <expand macro="output_option" name="msms" label="MSMS"/>
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101 <expand macro="output_option" name="mzTab" label="mzTab"/>
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102 <expand macro="output_option" name="allPeptides" label="all peptides"/>
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103 <expand macro="output_option" name="libraryMatch" label="library match"/>
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104 <expand macro="output_option" name="matchedFeatures"
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105 label="matched features"/>
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106 <expand macro="output_option" name="modificationSpecificPeptides"
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107 label="modification specific peptides"/>
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108 <expand macro="output_option" name="ms3Scans" label="ms3 scans"/>
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109 <expand macro="output_option" name="msmsScans" label="msms scans"/>
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110 <expand macro="output_option" name="mzRange" label="mz range"/>
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111 <expand macro="output_option" name="peptideSection" label="peptide section"/>
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112 <expand macro="output_option" name="summary" label="summary"/>
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113 <expand macro="output_option" name="output_all"
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114 label="complete 'combined/txt/' directory (compressed)"/>
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115 </param>
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116 </inputs>
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117
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118 <outputs>
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119 <expand macro="output" name="mqpar_out" label="mqpar.xml" format="xml"/>
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120 <expand macro="output" name="proteinGroups" label="MaxQuant Protein Groups"/>
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121 <expand macro="output" name="peptides" label="MaxQuant Peptides"/>
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122 <expand macro="output" name="evidence" label="MaxQuant Evidence"/>
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123 <expand macro="output" name="parameters" label="MaxQuant Tabular Parameters"/>
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124 <expand macro="output" name="msms" label="MaxQuant MSMS"/>
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125 <expand macro="output" name="mzTab" label="mzTab"/>
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126 <expand macro="output" name="allPeptides" label="all peptides"/>
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127 <expand macro="output" name="libraryMatch" label="library match"/>
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128 <expand macro="output" name="matchedFeatures" label="matched features"/>
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129 <expand macro="output" name="modificationSpecificPeptides"
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130 label="modification specific peptides"/>
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131 <expand macro="output" name="ms3Scans" label="ms3 scans"/>
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132 <expand macro="output" name="msmsScans"
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133 label="msms Scans"/>
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134 <expand macro="output" name="mzRange"
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135 label="mz range"/>
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136 <expand macro="output" name="peptideSection"
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137 label="peptide section"/>
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138 <expand macro="output" name="summary"
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139 label="MaxQuant summary"/>
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140 <expand macro="output" format="tar" name="output_all"
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141 label="'combined/txt/' directory"/>
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142 <data name="log" format="txt"
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143 label="log"/>
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144 </outputs>
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145
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146 <tests>
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147 <test>
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148 <param name="select" value="mzxml_files" />
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149 <param name="mzxml_files" value="BSA_min_22,BSA_min_21.mzXML" />
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150 <param name="fasta_files" value="bsa.fasta" />
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151 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
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152 <param name="description_parse_rule" value="&gt;(.*)" />
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153 <param name="mqpar_in" value="two/mqpar.xml" />
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154 <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides" />
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155 <output name="evidence" file="two/combined/txt/evidence.txt" />
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156 <output name="msms" file="two/combined/txt/msms.txt" />
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157 <output name="mzTab" file="two/combined/txt/mzTab.mzTab" lines_diff="4"/>
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158 <output name="allPeptides" file="two/combined/txt/allPeptides.txt" lines_diff="14"/>
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159 <output name="msmsScans" file="two/combined/txt/msmsScans.txt" />
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160 <output name="mzRange" file="two/combined/txt/mzRange.txt" />
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161 <output name="parameters" file="two/combined/txt/parameters.txt" lines_diff="8"/>
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162 <output name="peptides" file="two/combined/txt/peptides.txt" />
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163 <output name="peptideSection" file="two/combined/txt/peptideSection.txt" />
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164 <output name="proteinGroups" file="two/combined/txt/proteinGroups.txt" />
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165 <output name="summary" file="two/combined/txt/summary.txt" />
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166 <output name="modificationSpecificPeptides" file="two/combined/txt/modificationSpecificPeptides.txt" />
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167 </test>
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168 </tests>
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169 <help><![CDATA[
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170 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
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171
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172 This tool is a wrapper for MaxQuant v@VERSION@. It gets its search parameters from a previously created parameter file (mqpar.xml). A similiar tool that allows the specification of search parameters directly through galaxy is available as well and should be preferred.
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173
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174 **Input files**
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175
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176 - Thermo raw file or mzXML file
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177 - The datatype has to be 'thermo.raw' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
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178 - mqpar.xml:
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179 - MaxQuant parameters will be taken from the provided mqpar.xml file. This parameter file MUST be created using the same version of MaxQuant as is used by this tool. The correct version of MaxQuant can be obtained via the bioconda channel for the conda package manager.
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180
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181 **Output files**
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182
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183 Different output file options are available, most of them are part of the MaxQuant txt folder. An additional mztab output option is implemented.
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184 ]]></help>
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185 <citations>
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186 <citation type="bibtex">
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187 @article{cox2008maxquant,
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188 title={MaxQuant enables high peptide identification rates, individualized
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189 ppb-range mass accuracies and proteome-wide protein quantification},
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190 author={Cox, J{\"u}rgen and Mann, Matthias},
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191 journal={Nature biotechnology},
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192 volume={26},
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193 number={12},
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194 pages={1367},
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195 year={2008},
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196 publisher={Nature Publishing Group}
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197 }
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198 </citation>
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199 <citation type="bibtex">
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200 @article{tyanova2016maxquant,
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201 title={The MaxQuant computational platform for mass
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202 spectrometry-based shotgun proteomics},
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203 author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen},
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204 journal={Nature protocols},
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205 volume={11},
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206 number={12},
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207 pages={2301},
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208 year={2016},
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209 publisher={Nature Publishing Group}
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210 }
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211 </citation>
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212 </citations>
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213 </tool>