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comparison maxquant.xml @ 12:0839f84def5e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
author galaxyp
date Sun, 20 Jun 2021 16:37:41 +0000
parents d72c96ad9a16
children 181bd6a5f6ce
comparison
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11:d72c96ad9a16 12:0839f84def5e
1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy5"> 1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy@VERSION_SUFFIX@">
2 <macros> 2 <macros>
3 <xml name="output" token_format="tabular" token_label="default description" token_name="default"> 3 <xml name="output" token_format="tabular" token_label="default description" token_name="default">
4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> 4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
5 <filter>'@NAME@' in output_opts['output']</filter> 5 <filter>'@NAME@' in output_opts['output']</filter>
6 </data> 6 </data>
14 </macros> 14 </macros>
15 <expand macro="requirements"/> 15 <expand macro="requirements"/>
16 <command detect_errors="exit_code"><![CDATA[ 16 <command detect_errors="exit_code"><![CDATA[
17 #import re 17 #import re
18 maxquant -c mqpar.xml 2>/dev/null ## MQ writes success of creation to stderr 18 maxquant -c mqpar.xml 2>/dev/null ## MQ writes success of creation to stderr
19
20 ## Workaround for wrong MQ version in MaxQuantCmd.exe created mqpar.xml (1.6.5.0 instead of 1.6.17.0)
21 ## Should be removed as soon as MQ is updated with a fixed version
22 &&
23 sed -i -E 's:(maxQuantVersion>)1.6.5.0(<):\1'1.6.17.0'\2:' mqpar.xml
24 ## ==============================================================================================
25
19 #if 'config' in $output_opts.output: 26 #if 'config' in $output_opts.output:
20 && 27 &&
21 cp '$mq_conf' '$config' 28 cp '$mq_conf' '$config'
22 #end if 29 #end if
23 #set infiles = [$name for $pg in $paramGroups for $name in $pg.files] 30 #set infiles = [$name for $pg in $paramGroups for $name in $pg.files]
153 - [] 160 - []
154 #end if 161 #end if
155 #end if 162 #end if
156 #if $pg.quant_method.select_quant_method == 'lfq': 163 #if $pg.quant_method.select_quant_method == 'lfq':
157 lfqMode: 1 164 lfqMode: 1
158 lfqSkipNorm: ${pg.quant_method.lfqSkipNorm} 165 lfqNormType: ${pg.quant_method.lfqNormType}
159 lfqMinEdgesPerNode: ${pg.quant_method.lfqMinEdgesPerNode} 166 lfqMinEdgesPerNode: ${pg.quant_method.lfqMinEdgesPerNode}
160 lfqAvEdgesPerNode: ${pg.quant_method.lfqAvEdgesPerNode} 167 lfqAvEdgesPerNode: ${pg.quant_method.lfqAvEdgesPerNode}
161 lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount} 168 lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount}
162 #end if 169 #end if
163 #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2': 170 #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2':
190 @TMT10PLEX@ 197 @TMT10PLEX@
191 #end if 198 #end if
192 #if $pg.quant_method.iso_labels.labeling == 'tmt11plex': 199 #if $pg.quant_method.iso_labels.labeling == 'tmt11plex':
193 @TMT11PLEX@ 200 @TMT11PLEX@
194 #end if 201 #end if
202 #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex':
203 @TMTPRO16PLEX@
204 #end if
195 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': 205 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex':
196 @ITRAQ4PLEX@ 206 @ITRAQ4PLEX@
197 #end if 207 #end if
198 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex': 208 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex':
199 @ITRAQ8PLEX@ 209 @ITRAQ8PLEX@
231 #if $pg.quant_method.iso_labels.labeling == 'tmt10plex': 241 #if $pg.quant_method.iso_labels.labeling == 'tmt10plex':
232 @TMT10PLEX@ 242 @TMT10PLEX@
233 #end if 243 #end if
234 #if $pg.quant_method.iso_labels.labeling == 'tmt11plex': 244 #if $pg.quant_method.iso_labels.labeling == 'tmt11plex':
235 @TMT11PLEX@ 245 @TMT11PLEX@
246 #end if
247 #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex':
248 @TMTPRO16PLEX@
236 #end if 249 #end if
237 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': 250 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex':
238 @ITRAQ4PLEX@ 251 @ITRAQ4PLEX@
239 #end if 252 #end if
240 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex': 253 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex':
475 label="LFQ minimum number of neighbours" value="3" 488 label="LFQ minimum number of neighbours" value="3"
476 help="Defines the network to normalize the samples in the fast LFQ mode."/> 489 help="Defines the network to normalize the samples in the fast LFQ mode."/>
477 <param type="integer" name="lfqAvEdgesPerNode" 490 <param type="integer" name="lfqAvEdgesPerNode"
478 label="LFQ average number of neighbours" value="6" 491 label="LFQ average number of neighbours" value="6"
479 help="Defines the network to normalize the samples in the fast LFQ mode."/> 492 help="Defines the network to normalize the samples in the fast LFQ mode."/>
480 <param type="boolean" name="lfqSkipNorm" checked="true" 493 <param name="lfqNormType" type="select" label="Normalization type"
481 label="Skip normalization" 494 multiple="false" help="">
482 truevalue="True" falsevalue="False" 495 <option value="0">None</option>
483 help="If checked the high-speed version of MaxLFQ is used. This is recommended for large numbers of samples (Experiments). For less than 10 samples the original MaxLFQ normalization algorithm is used."/> 496 <option value="1">Classic</option>
497 </param>
484 </when> 498 </when>
485 <when value="reporter_ion_ms2"> 499 <when value="reporter_ion_ms2">
486 <conditional name="iso_labels"> 500 <conditional name="iso_labels">
487 <param name="labeling" type="select" label="isobaric labeling" 501 <param name="labeling" type="select" label="isobaric labeling"
488 help="Select one of the standard labelings (correction factors are zero) or create a custom labeling."> 502 help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">
490 <option value="tmt2plex">TMT2plex</option> 504 <option value="tmt2plex">TMT2plex</option>
491 <option value="tmt6plex">TMT6plex</option> 505 <option value="tmt6plex">TMT6plex</option>
492 <option value="tmt8plex">TMT8plex</option> 506 <option value="tmt8plex">TMT8plex</option>
493 <option value="tmt10plex">TMT10plex</option> 507 <option value="tmt10plex">TMT10plex</option>
494 <option value="tmt11plex">TMT11plex</option> 508 <option value="tmt11plex">TMT11plex</option>
509 <option value="tmtpro16plex">TMTpro16plex</option>
495 <option value="itraq4plex">iTRAQ4plex</option> 510 <option value="itraq4plex">iTRAQ4plex</option>
496 <option value="itraq8plex">iTRAQ8plex</option> 511 <option value="itraq8plex">iTRAQ8plex</option>
497 <option value="iodotmt6plex">iodoTMT6plex</option> 512 <option value="iodotmt6plex">iodoTMT6plex</option>
498 </param> 513 </param>
499 <when value="tmt2plex"/> 514 <when value="tmt2plex"/>
500 <when value="tmt6plex"/> 515 <when value="tmt6plex"/>
501 <when value="tmt8plex"/> 516 <when value="tmt8plex"/>
502 <when value="tmt10plex"/> 517 <when value="tmt10plex"/>
503 <when value="tmt11plex"/> 518 <when value="tmt11plex"/>
519 <when value="tmtpro16plex"/>
504 <when value="itraq4plex"/> 520 <when value="itraq4plex"/>
505 <when value="itraq8plex"/> 521 <when value="itraq8plex"/>
506 <when value="iodotmt6plex"/> 522 <when value="iodotmt6plex"/>
507 <when value="custom"> 523 <when value="custom">
508 <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> 524 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
543 <option value="tmt2plex">TMT2plex</option> 559 <option value="tmt2plex">TMT2plex</option>
544 <option value="tmt6plex">TMT6plex</option> 560 <option value="tmt6plex">TMT6plex</option>
545 <option value="tmt8plex">TMT8plex</option> 561 <option value="tmt8plex">TMT8plex</option>
546 <option value="tmt10plex">TMT10plex</option> 562 <option value="tmt10plex">TMT10plex</option>
547 <option value="tmt11plex">TMT11plex</option> 563 <option value="tmt11plex">TMT11plex</option>
564 <option value="tmtpro16plex">TMTpro16plex</option>
548 <option value="itraq4plex">iTRAQ4plex</option> 565 <option value="itraq4plex">iTRAQ4plex</option>
549 <option value="itraq8plex">iTRAQ8plex</option> 566 <option value="itraq8plex">iTRAQ8plex</option>
550 <option value="iodotmt6plex">iodoTMT6plex</option> 567 <option value="iodotmt6plex">iodoTMT6plex</option>
551 </param> 568 </param>
552 <when value="tmt2plex"/> 569 <when value="tmt2plex"/>
553 <when value="tmt6plex"/> 570 <when value="tmt6plex"/>
554 <when value="tmt8plex"/> 571 <when value="tmt8plex"/>
555 <when value="tmt10plex"/> 572 <when value="tmt10plex"/>
556 <when value="tmt11plex"/> 573 <when value="tmt11plex"/>
574 <when value="tmtpro16plex"/>
557 <when value="itraq4plex"/> 575 <when value="itraq4plex"/>
558 <when value="itraq8plex"/> 576 <when value="itraq8plex"/>
559 <when value="iodotmt6plex"/> 577 <when value="iodotmt6plex"/>
560 <when value="custom"> 578 <when value="custom">
561 <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> 579 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
641 </repeat> 659 </repeat>
642 <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,output_all,config,mqpar" /> 660 <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,output_all,config,mqpar" />
643 <output name="mqpar" file="01/mqpar.xml" lines_diff="6"/> 661 <output name="mqpar" file="01/mqpar.xml" lines_diff="6"/>
644 <output name="evidence" file="01/combined/txt/evidence.txt" /> 662 <output name="evidence" file="01/combined/txt/evidence.txt" />
645 <output name="msms" file="01/combined/txt/msms.txt" /> 663 <output name="msms" file="01/combined/txt/msms.txt" />
646 <output name="mzTab" file="01/combined/txt/mzTab.mzTab" lines_diff="4"/> 664 <output name="mzTab" file="01/combined/txt/mzTab.mzTab" lines_diff="34"/>
647 <output name="allPeptides" file="01/combined/txt/allPeptides.txt" lines_diff="4"/> 665 <output name="allPeptides" file="01/combined/txt/allPeptides.txt" lines_diff="2"/>
648 <output name="msmsScans" file="01/combined/txt/msmsScans.txt" lines_diff="8"/> 666 <output name="msmsScans" file="01/combined/txt/msmsScans.txt" lines_diff="8"/>
649 <output name="mzRange" file="01/combined/txt/mzRange.txt" /> 667 <output name="mzRange" file="01/combined/txt/mzRange.txt" />
650 <output name="parameters" file="01/combined/txt/parameters.txt" lines_diff="10"/> 668 <output name="parameters" file="01/combined/txt/parameters.txt" lines_diff="10"/>
651 <output name="peptides" file="01/combined/txt/peptides.txt" /> 669 <output name="peptides" file="01/combined/txt/peptides.txt" />
652 <output name="peptideSection" file="01/combined/txt/peptideSection.txt" /> 670 <output name="peptideSection" file="01/combined/txt/peptideSection.txt" />
877 <output name="mqpar" file="04/mqpar.xml" lines_diff="12" /> 895 <output name="mqpar" file="04/mqpar.xml" lines_diff="12" />
878 </test> 896 </test>
879 <!-- PTXQC Test --> 897 <!-- PTXQC Test -->
880 <test expect_num_outputs="3"> 898 <test expect_num_outputs="3">
881 <param name="ftype" value=".mzxml" /> 899 <param name="ftype" value=".mzxml" />
882 <param name="fasta_files" value="ptxqc.fasta" /> 900 <param name="fasta_files" value="tmt_data.fasta" />
883 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 901 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
884 <param name="description_parse_rule" value="&gt;(.*)" /> 902 <param name="description_parse_rule" value="&gt;(.*)" />
885 <repeat name="paramGroups"> 903 <repeat name="paramGroups">
886 <param name="files" value="ptxqc.mzXML"/> 904 <param name="files" value="tmt_data.mzXML"/>
887 <param name="variableModifications" value="Oxidation (M)" /> 905 <param name="variableModifications" value="Oxidation (M)" />
888 <param name="fixedModifications" value="" /> 906 <param name="fixedModifications" value="" />
889 <conditional name="quant_method"> 907 <conditional name="quant_method">
890 <param name="select_quant_method" value="reporter_ion_ms2" /> 908 <param name="select_quant_method" value="reporter_ion_ms2" />
891 <conditional name="iso_labels"> 909 <conditional name="iso_labels">
895 </repeat> 913 </repeat>
896 <param name="do_it" value="True" /> 914 <param name="do_it" value="True" />
897 <param name="output" value="config,mqpar" /> 915 <param name="output" value="config,mqpar" />
898 <output name="config" file="07/config.yml" lines_diff="2" /> 916 <output name="config" file="07/config.yml" lines_diff="2" />
899 <!-- high difference due to unconsistant xml formatting in MQ --> 917 <!-- high difference due to unconsistant xml formatting in MQ -->
900 <output name="mqpar" file="07/mqpar.xml" lines_diff="24" /> 918 <output name="mqpar" file="07/mqpar.xml" lines_diff="4" />
901 <output name="ptxqc_report" file="07/combined/txt/report_v1.0.9_combined.pdf" compare="sim_size" /> 919 <output name="ptxqc_report" file="07/combined/txt/report_v1.0.10_combined.pdf" compare="sim_size" />
920 </test>
921 <!-- TMTpro16plex test -->
922 <test expect_num_outputs="3">
923 <param name="ftype" value=".mzxml" />
924 <param name="fasta_files" value="tmt_data_16.fasta" />
925 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
926 <param name="description_parse_rule" value="&gt;(.*)" />
927 <repeat name="paramGroups">
928 <param name="files" value="tmt_data.mzXML"/>
929 <param name="variableModifications" value="Oxidation (M)" />
930 <param name="fixedModifications" value="" />
931 <conditional name="quant_method">
932 <param name="select_quant_method" value="reporter_ion_ms2" />
933 <conditional name="iso_labels">
934 <param name="labeling" value="tmtpro16plex" />
935 </conditional>
936 </conditional>
937 </repeat>
938 <param name="do_it" value="False" />
939 <param name="output" value="config,mqpar,proteinGroups" />
940 <output name="config" file="08/config.yml" lines_diff="2" />
941 <!-- high difference due to unconsistant xml formatting in MQ -->
942 <output name="mqpar" file="08/mqpar.xml" lines_diff="24" />
943 <output name="proteinGroups" file="08/combined/txt/proteinGroups.txt" />
902 </test> 944 </test>
903 </tests> 945 </tests>
904 946
905 <help><![CDATA[ 947 <help><![CDATA[
906 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. 948 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.