Mercurial > repos > galaxyp > maxquant_mqpar

annotate maxquant_mqpar.xml @ 4:d0485bab76b8 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
author galaxyp
date Fri, 19 Feb 2021 21:24:09 +0000
parents f9c1f29d9711
children
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a52165553917 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@">
a52165553917 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@">
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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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">
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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9 <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="@LABEL@ for ${on_string}" name="@NAME@">
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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10 <filter>'@NAME@' in output</filter>
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11 </data>
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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12 </xml>
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a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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13 <import>macros.xml</import>
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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14 </macros>
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15 <expand macro="requirements"/>
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a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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16 <command detect_errors="exit_code"><![CDATA[
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17 ## link galaxy datasets to filenames accepted by maxquant
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18 #import re
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19 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $input.infiles]
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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20 #set names_with_ext = [($name if ($name).lower().endswith(str($input.ftype)) else $name + str($input.ftype)) for $name in $names]
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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21 #for $target, $link in zip($infiles, $names_with_ext)
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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22 ln -s '$target' '$link' &&
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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23 #end for
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24
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25 python3 '$__tool_directory__/modify_mqpar.py'
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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26 #set inf = ','.join($names_with_ext)
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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27 --infiles='$inf'
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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28 --version=@VERSION@
0
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29 --num_threads=\${GALAXY_SLOTS:-1}
a52165553917 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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30 --substitution_rx='@SUBSTITUTION_RX@'
a52165553917 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='$identifier_parse_rule'
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34 '$mqpar_input'
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35
3
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36 &&
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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37 maxquant mqpar.xml
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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38 #if 'log' in $output:
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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39 >> '$log'
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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40 #end if
4
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41 && mv mqpar.xml combined/txt/mqpar.xml
3
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42 #if 'output_all' in $output:
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43 &&
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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44 tar -zcf '$output_all' ./combined/txt
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45 #end if
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46
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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47 #if $qc.do_it:
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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48 &&
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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49 Rscript '$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>
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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>
4
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105 <param type="data" name="mqpar_input" 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."/>
3
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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">
3
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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;(.*)" />
4
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144 <param name="mqpar_input" value="mqpar.xml" />
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145 <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" />
3
f9c1f29d9711 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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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" />
4
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156 <output name="mqpar" file="txt/mqpar.xml" lines_diff="8" />
0
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157 </test>
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158 </tests>
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159 <help><![CDATA[
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160 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
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161
3
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162 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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163
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164 **Input files**
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165
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166 - Thermo raw file or mzXML file
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167 - 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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168 - mqpar.xml:
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169 - 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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170
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171 **Output files**
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173 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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174 ]]></help>
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175 <expand macro="citations"/>
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176 </tool>