Mercurial > repos > galaxyp > maxquant_mqpar

annotate maxquant_mqpar.xml @ 3:2d67fb758956 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
author galaxyp
date Sat, 11 Apr 2020 11:50:09 -0400
parents 3fc2116ac6d9
children 9cb7dcc07dae
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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@">
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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2 <macros>
3
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3 <xml name="output" token_format="tabular" token_label="default description" token_name="default">
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4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
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5 <filter>'@NAME@' in output</filter>
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6 </data>
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7 </xml>
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8 <xml name="output_from_wdir" token_ext="txt" token_format="tabular" token_label="default description" token_name="default">
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9 <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="@LABEL@ for ${on_string}" name="@NAME@">
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10 <filter>'@NAME@' in output</filter>
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11 </data>
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12 </xml>
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256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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13 <import>macros.xml</import>
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14 </macros>
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15 <expand macro="requirements"/>
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16 <command detect_errors="exit_code"><![CDATA[
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17 ## link galaxy datasets to filenames accepted by maxquant
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18 #import re
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19 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $input.infiles]
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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20 #set names_with_ext = [($name if ($name).lower().endswith(str($input.ftype)) else $name + str($input.ftype)) for $name in $names]
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21 #for $target, $link in zip($infiles, $names_with_ext)
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22 ln -s '$target' '$link' &&
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23 #end for
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24
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25 python3 '$__tool_directory__/modify_mqpar.py'
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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26 #set inf = ','.join($names_with_ext)
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27 --infiles='$inf'
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28 --version=@VERSION@
0
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29 --num_threads=\${GALAXY_SLOTS:-1}
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30 --substitution_rx='@SUBSTITUTION_RX@'
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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31 --fasta_files='$fasta_files'
3
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32 --description_parse_rule='$description_parse_rule'
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33 --identifier_parse_rule='$identifier_parse_rule'
3
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34 '$mqpar'
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35
3
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36 &&
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37 maxquant mqpar.xml
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38 #if 'log' in $output:
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39 >> '$log'
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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40 #end if
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41 && mv '$mqpar' combined/txt/mqpar.xml
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42 #if 'output_all' in $output:
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43 &&
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44 tar -zcf '$output_all' ./combined/txt
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45 #end if
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46
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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47 #if $qc.do_it:
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48 &&
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49 Rscript '$qr' '$qr_yaml'
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50 #if 'log' in $output:
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51 >> '$log' 2>&1
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52 #end if
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53 &&
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54 cp ./combined/txt/report_v0.92.6_combined.pdf '$ptxqc_report'
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55 #end if
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56 ]]></command>
0
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57
3
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58 <configfiles>
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59 <expand macro="ptxqc"/>
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60 </configfiles>
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61
0
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62 <inputs>
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63 <conditional name="input">
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64 <param name="ftype" type="select" label="choose the type of your input files">
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65 <option value=".thermo.raw">thermo.raw</option>
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66 <option value=".mzxml">mzXML</option>
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67 <option value=".mzml">mzML</option>
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68 </param>
3
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69 <when value=".thermo.raw">
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70 <param multiple="true" name="infiles" type="data"
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71 format="thermo.raw" label="RAW Files"
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72 help="Specify one or more Thermo RAW files" />
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73 </when>
3
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74 <when value=".mzxml">
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75 <param multiple="true" name="infiles" type="data"
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76 format="mzXML" label="mzXML Files"
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77 help="Specify one or more mzXML files" />
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78 </when>
3
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79 <when value=".mzml">
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80 <param multiple="true" name="infiles" type="data"
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81 format="mzML" label="mzML Files"
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82 help="Specify one or more mzML files" />
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83 </when>
0
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84 </conditional>
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85 <param format="fasta" multiple="true" name="fasta_files"
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86 type="data" label="FASTA files"
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87 help="Specify one or more FASTA databases." />
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88 <param name="identifier_parse_rule" type="text"
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89 label="identifier parse rule" value="^&gt;.*\|(.*)\|.*$">
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90 <sanitizer>
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91 <valid initial="string.printable">
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92 <remove value="&apos;"/>
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93 </valid>
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94 </sanitizer>
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95 </param>
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96 <param name="description_parse_rule" type="text"
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97 label="description parse rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$"
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98 help="Modify parse rules if needed">
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99 <sanitizer>
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100 <valid initial="string.printable">
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101 <remove value="&apos;"/>
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102 </valid>
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103 </sanitizer>
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104 </param>
3
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105 <param type="data" name="mqpar" format="xml"
0
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106 label="mqpar.xml file with your search parameters. RAW file names
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107 must match the names displayed in galaxy. Their paths
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108 from the local machine are ignored. E.g. a file named
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109 'test01.raw' in galaxy can either be named 'test01.raw' or
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110 'D:\path\to\test01.raw' in the mqpar.xml."/>
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111 <expand macro="ptxqc-opts"/>
0
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112 <param type="select" name="output" label="Select the desired outputs."
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113 multiple="true" optional="false">
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114 <option value="proteinGroups">Protein Groups</option>
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115 <option value="mqpar">mqpar.xml</option>
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116 <option value="peptides">Peptides</option>
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117 <option value="evidence">Evidence</option>
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118 <option value="parameters">Tabular Paramters</option>
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119 <option value="msms">MSMS</option>
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120 <option value="mzTab">mzTab</option>
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121 <option value="allPeptides">all peptides</option>
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122 <option value="libraryMatch">library match</option>
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123 <option value="matchedFeatures">matched features</option>
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124 <option value="modificationSpecificPeptides">modification specific peptides</option>
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125 <option value="ms3Scans">ms3 scans</option>
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126 <option value="msmsScans">msms scans</option>
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127 <option value="mzRange">mz range</option>
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128 <option value="peptideSection">peptide section</option>
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129 <option value="summary">summary</option>
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130 <option value="output_all">complete 'combined/txt/' directory (compressed)</option>
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131 <option value="log">MaxQuant and PTXQC log</option>
0
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132 </param>
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133 </inputs>
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134
3
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135 <expand macro="outputs"/>
0
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136
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137 <tests>
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138 <test>
3
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139 <param name="ftype" value=".mzxml" />
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140 <param name="infiles" value="BSA_min_22,BSA_min_21.mzXML" />
0
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141 <param name="fasta_files" value="bsa.fasta" />
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142 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
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143 <param name="description_parse_rule" value="&gt;(.*)" />
3
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144 <param name="mqpar" value="mqpar.xml" />
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145 <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,output_all" />
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146 <output name="evidence" file="txt/evidence.txt" />
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147 <output name="msms" file="txt/msms.txt" lines_diff="2" />
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148 <output name="allPeptides" file="txt/allPeptides.txt" lines_diff="32" />
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149 <output name="msmsScans" file="txt/msmsScans.txt" lines_diff="4"/>
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150 <output name="mzRange" file="txt/mzRange.txt" />
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151 <output name="parameters" file="txt/parameters.txt" lines_diff="8"/>
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152 <output name="peptides" file="txt/peptides.txt" />
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153 <output name="proteinGroups" file="txt/proteinGroups.txt" />
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154 <output name="summary" file="txt/summary.txt" />
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155 <output name="modificationSpecificPeptides" file="txt/modificationSpecificPeptides.txt" />
0
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156 </test>
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157 </tests>
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158 <help><![CDATA[
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159 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
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160
3
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161 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, if possible.
0
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162
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163 **Input files**
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164
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165 - Thermo raw file or mzXML file
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166 - 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)
2
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167 - mqpar.xml:
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168 - 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.
0
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169
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170 **Output files**
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171
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172 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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173 ]]></help>
3
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174 <expand macro="citations"/>
0
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175 </tool>