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comparison maxquant.xml @ 10:68d8dcdbddb1 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
author galaxyp
date Tue, 15 Jun 2021 07:55:19 +0000
parents fe479bf15bd3
children 057bf124c80e
comparison
equal deleted inserted replaced
9:fe479bf15bd3 10:68d8dcdbddb1
1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy4"> 1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy5">
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 ${on_string}" name="@NAME@">
5 <filter>'@NAME@' in output_opts['output']</filter> 5 <filter>'@NAME@' in output_opts['output']</filter>
6 </data> 6 </data>
61 Rscript '$qr' '$qr_yaml' 61 Rscript '$qr' '$qr_yaml'
62 #if 'log' in $output_opts.output: 62 #if 'log' in $output_opts.output:
63 >> '$log' 2>&1 63 >> '$log' 2>&1
64 #end if 64 #end if
65 && 65 &&
66 cp ./combined/txt/report_v0.92.6_combined.pdf '$ptxqc_report' 66 cp './combined/txt/report_v@VERSION_PTXQC@_combined.pdf' '$ptxqc_report'
67 #end if 67 #end if
68 #end if 68 #end if
69 ]]></command> 69 ]]></command>
70 70
71 <configfiles> 71 <configfiles>
176 #for $l in $pg.quant_method.iso_labels.iso_label: 176 #for $l in $pg.quant_method.iso_labels.iso_label:
177 - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike] 177 - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike]
178 #end for 178 #end for
179 #end if 179 #end if
180 #if $pg.quant_method.iso_labels.labeling == 'tmt2plex': 180 #if $pg.quant_method.iso_labels.labeling == 'tmt2plex':
181 - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] 181 @TMT2PLEX@
182 - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]
183 #end if 182 #end if
184 #if $pg.quant_method.iso_labels.labeling == 'tmt6plex': 183 #if $pg.quant_method.iso_labels.labeling == 'tmt6plex':
185 - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True] 184 @TMT6PLEX@
186 - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True]
187 - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True]
188 - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True]
189 - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True]
190 - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True]
191 #end if 185 #end if
192 #if $pg.quant_method.iso_labels.labeling == 'tmt8plex': 186 #if $pg.quant_method.iso_labels.labeling == 'tmt8plex':
193 - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True] 187 @TMT8PLEX@
194 - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True]
195 - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True]
196 - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True]
197 - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True]
198 - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True]
199 - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True]
200 - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True]
201 #end if 188 #end if
202 #if $pg.quant_method.iso_labels.labeling == 'tmt10plex': 189 #if $pg.quant_method.iso_labels.labeling == 'tmt10plex':
203 @TMT10PLEX@ 190 @TMT10PLEX@
204 #end if 191 #end if
205 #if $pg.quant_method.iso_labels.labeling == 'tmt11plex': 192 #if $pg.quant_method.iso_labels.labeling == 'tmt11plex':
206 @TMT10PLEX@ 193 @TMT11PLEX@
207 - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True]
208 #end if 194 #end if
209 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': 195 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex':
210 - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] 196 @ITRAQ4PLEX@
211 - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]
212 - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]
213 - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False]
214 #end if 197 #end if
215 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex': 198 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex':
216 - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False] 199 @ITRAQ8PLEX@
217 - [iTRAQ4plex-Lys114,iTRAQ8plex-Nter114,0,0,0,0,False]
218 - [iTRAQ4plex-Lys115,iTRAQ8plex-Nter115,0,0,0,0,False]
219 - [iTRAQ4plex-Lys116,iTRAQ8plex-Nter116,0,0,0,0,False]
220 - [iTRAQ4plex-Lys117,iTRAQ8plex-Nter117,0,0,0,0,False]
221 - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False]
222 - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False]
223 - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False]
224 #end if 200 #end if
225 #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex': 201 #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex':
226 - [iodoTMT6plex-Cys126,'',0,0,0,0,True] 202 @IODOTMT6PLEX@
227 - [iodoTMT6plex-Cys127,'',0,0,0,0,True]
228 - [iodoTMT6plex-Cys128,'',0,0,0,0,True]
229 - [iodoTMT6plex-Cys129,'',0,0,0,0,True]
230 - [iodoTMT6plex-Cys130,'',0,0,0,0,True]
231 - [iodoTMT6plex-Cys131,'',0,0,0,0,True]
232 #end if 203 #end if
233 #end if 204 #end if
234 #if $pg.quant_method.select_quant_method == 'reporter_ion_ms3': 205 #if $pg.quant_method.select_quant_method == 'reporter_ion_ms3':
235 lcmsRunType: 'Reporter ion MS3' 206 lcmsRunType: 'Reporter ion MS3'
236 reporterMassTolerance: 0.003 207 reporterMassTolerance: 0.003
246 #if $pg.quant_method.iso_labels.labeling == 'custom': 217 #if $pg.quant_method.iso_labels.labeling == 'custom':
247 #for $l in $pg.quant_method.iso_labels.iso_label: 218 #for $l in $pg.quant_method.iso_labels.iso_label:
248 - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike] 219 - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike]
249 #end for 220 #end for
250 #end if 221 #end if
251 #if $pg.quant_method.iso_labels.labeling == 'tmt2plex': 222 #if $pg.quant_method.iso_labels.labeling == 'tmt2plex':
252 - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] 223 @TMT2PLEX@
253 - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]
254 #end if 224 #end if
255 #if $pg.quant_method.iso_labels.labeling == 'tmt6plex': 225 #if $pg.quant_method.iso_labels.labeling == 'tmt6plex':
256 - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True] 226 @TMT6PLEX@
257 - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True]
258 - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True]
259 - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True]
260 - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True]
261 - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True]
262 #end if 227 #end if
263 #if $pg.quant_method.iso_labels.labeling == 'tmt8plex': 228 #if $pg.quant_method.iso_labels.labeling == 'tmt8plex':
264 - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True] 229 @TMT8PLEX@
265 - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True]
266 - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True]
267 - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True]
268 - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True]
269 - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True]
270 - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True]
271 - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True]
272 #end if 230 #end if
273 #if $pg.quant_method.iso_labels.labeling == 'tmt10plex': 231 #if $pg.quant_method.iso_labels.labeling == 'tmt10plex':
274 @TMT10PLEX@ 232 @TMT10PLEX@
275 #end if 233 #end if
276 #if $pg.quant_method.iso_labels.labeling == 'tmt11plex': 234 #if $pg.quant_method.iso_labels.labeling == 'tmt11plex':
277 @TMT10PLEX@ 235 @TMT11PLEX@
278 - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True]
279 #end if 236 #end if
280 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': 237 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex':
281 - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] 238 @ITRAQ4PLEX@
282 - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]
283 - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]
284 - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False]
285 #end if 239 #end if
286 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex': 240 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex':
287 - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False] 241 @ITRAQ8PLEX@
288 - [iTRAQ4plex-Lys114,iTRAQ8plex-Nter114,0,0,0,0,False]
289 - [iTRAQ4plex-Lys115,iTRAQ8plex-Nter115,0,0,0,0,False]
290 - [iTRAQ4plex-Lys116,iTRAQ8plex-Nter116,0,0,0,0,False]
291 - [iTRAQ4plex-Lys117,iTRAQ8plex-Nter117,0,0,0,0,False]
292 - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False]
293 - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False]
294 - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False]
295 #end if 242 #end if
296 #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex': 243 #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex':
297 - [iodoTMT6plex-Cys126,'',0,0,0,0,True] 244 @IODOTMT6PLEX@
298 - [iodoTMT6plex-Cys127,'',0,0,0,0,True]
299 - [iodoTMT6plex-Cys128,'',0,0,0,0,True]
300 - [iodoTMT6plex-Cys129,'',0,0,0,0,True]
301 - [iodoTMT6plex-Cys130,'',0,0,0,0,True]
302 - [iodoTMT6plex-Cys131,'',0,0,0,0,True]
303 #end if 245 #end if
304 #end if 246 #end if
305 #end for 247 #end for
306 </configfile> 248 </configfile>
307 <expand macro="ptxqc"/> 249 <expand macro="ptxqc"/>
552 <option value="tmt11plex">TMT11plex</option> 494 <option value="tmt11plex">TMT11plex</option>
553 <option value="itraq4plex">iTRAQ4plex</option> 495 <option value="itraq4plex">iTRAQ4plex</option>
554 <option value="itraq8plex">iTRAQ8plex</option> 496 <option value="itraq8plex">iTRAQ8plex</option>
555 <option value="iodotmt6plex">iodoTMT6plex</option> 497 <option value="iodotmt6plex">iodoTMT6plex</option>
556 </param> 498 </param>
557 499 <when value="tmt2plex"/>
558 <when value="tmt2plex"></when> 500 <when value="tmt6plex"/>
559 <when value="tmt6plex"></when> 501 <when value="tmt8plex"/>
560 <when value="tmt8plex"></when> 502 <when value="tmt10plex"/>
561 <when value="tmt10plex"></when> 503 <when value="tmt11plex"/>
562 <when value="tmt11plex"></when> 504 <when value="itraq4plex"/>
563 <when value="itraq4plex"></when> 505 <when value="itraq8plex"/>
564 <when value="itraq8plex"></when> 506 <when value="iodotmt6plex"/>
565 <when value="iodotmt6plex"></when>
566 <when value="custom"> 507 <when value="custom">
567 <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> 508 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
568 <param name="internallabel" type="select" label="internal label" help="contains Lys"> 509 <param name="internallabel" type="select" label="internal label" help="contains Lys">
569 <expand macro="iso_labels"/> 510 <expand macro="iso_labels"/>
570 </param> 511 </param>
589 <when value="True"> 530 <when value="True">
590 <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0" 531 <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0"
591 max="1" 532 max="1"
592 help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/> 533 help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
593 </when> 534 </when>
594 <when value="False"></when> 535 <when value="False"/>
595 </conditional> 536 </conditional>
596 </when> 537 </when>
597 <when value="reporter_ion_ms3"> 538 <when value="reporter_ion_ms3">
598 <conditional name="iso_labels"> 539 <conditional name="iso_labels">
599 <param name="labeling" type="select" label="isobaric labeling" 540 <param name="labeling" type="select" label="isobaric labeling"
606 <option value="tmt11plex">TMT11plex</option> 547 <option value="tmt11plex">TMT11plex</option>
607 <option value="itraq4plex">iTRAQ4plex</option> 548 <option value="itraq4plex">iTRAQ4plex</option>
608 <option value="itraq8plex">iTRAQ8plex</option> 549 <option value="itraq8plex">iTRAQ8plex</option>
609 <option value="iodotmt6plex">iodoTMT6plex</option> 550 <option value="iodotmt6plex">iodoTMT6plex</option>
610 </param> 551 </param>
611 552 <when value="tmt2plex"/>
612 <when value="tmt2plex"></when> 553 <when value="tmt6plex"/>
613 <when value="tmt6plex"></when> 554 <when value="tmt8plex"/>
614 <when value="tmt8plex"></when> 555 <when value="tmt10plex"/>
615 <when value="tmt10plex"></when> 556 <when value="tmt11plex"/>
616 <when value="tmt11plex"></when> 557 <when value="itraq4plex"/>
617 <when value="itraq4plex"></when> 558 <when value="itraq8plex"/>
618 <when value="itraq8plex"></when> 559 <when value="iodotmt6plex"/>
619 <when value="iodotmt6plex"></when>
620 <when value="custom"> 560 <when value="custom">
621 <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> 561 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
622 <param name="internallabel" type="select" label="internal label" help="contains Lys"> 562 <param name="internallabel" type="select" label="internal label" help="contains Lys">
623 <expand macro="iso_labels"/> 563 <expand macro="iso_labels"/>
624 </param> 564 </param>
643 <when value="True"> 583 <when value="True">
644 <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0" 584 <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0"
645 max="1" 585 max="1"
646 help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/> 586 help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
647 </when> 587 </when>
648 <when value="False"></when> 588 <when value="False"/>
649 </conditional> 589 </conditional>
650 </when> 590 </when>
651 </conditional> 591 </conditional>
652 </repeat> 592 </repeat>
653 593
661 multiple="true" optional="false"> 601 multiple="true" optional="false">
662 <option value="proteinGroups">Protein Groups</option> 602 <option value="proteinGroups">Protein Groups</option>
663 <option value="mqpar">mqpar.xml</option> 603 <option value="mqpar">mqpar.xml</option>
664 <option value="peptides">Peptides</option> 604 <option value="peptides">Peptides</option>
665 <option value="evidence">Evidence</option> 605 <option value="evidence">Evidence</option>
666 <option value="parameters">Tabular Paramters</option> 606 <option value="parameters">Tabular Parameters</option>
667 <option value="msms">MSMS</option> 607 <option value="msms">MSMS</option>
668 <option value="mzTab">mzTab</option> 608 <option value="mzTab">mzTab</option>
669 <option value="allPeptides">all peptides</option> 609 <option value="allPeptides">all peptides</option>
670 <option value="libraryMatch">library match</option> 610 <option value="libraryMatch">library match</option>
671 <option value="matchedFeatures">matched features</option> 611 <option value="matchedFeatures">matched features</option>
778 </conditional> 718 </conditional>
779 </conditional> 719 </conditional>
780 </repeat> 720 </repeat>
781 <param name="dry_run" value="True" /> 721 <param name="dry_run" value="True" />
782 <param name="output" value="config,mqpar,mzTab" /> 722 <param name="output" value="config,mqpar,mzTab" />
783 <output name="config" file="02/config.yml" lines_diff="2" /> 723 <output name="config" file="02/config.yml" lines_diff="7" />
784 <!-- high difference due to unconsistant xml formatting in MQ --> 724 <!-- high difference due to unconsistant xml formatting in MQ -->
785 <output name="mqpar" file="02/mqpar.xml" lines_diff="24" /> 725 <output name="mqpar" file="02/mqpar.xml" lines_diff="24" />
786 </test> 726 </test>
787 <!-- reporter ion ms3 + multiple param groups, testing yaml conf file and mqpar.xml only --> 727 <!-- reporter ion ms3 + multiple param groups, testing yaml conf file and mqpar.xml only -->
788 <test expect_num_outputs="3"> 728 <test expect_num_outputs="3">
847 </conditional> 787 </conditional>
848 </conditional> 788 </conditional>
849 </repeat> 789 </repeat>
850 <param name="dry_run" value="True" /> 790 <param name="dry_run" value="True" />
851 <param name="output" value="config,mqpar,mzTab" /> 791 <param name="output" value="config,mqpar,mzTab" />
852 <output name="config" file="06/config.yml" lines_diff="2"> 792 <output name="config" file="06/config.yml" lines_diff="7">
853 <assert_contents> 793 <assert_contents>
854 <has_text_matching expression="lcmsRunType\: \'Reporter ion MS3\'" /> 794 <has_text_matching expression="lcmsRunType\: \'Reporter ion MS3\'" />
855 </assert_contents> 795 </assert_contents>
856 </output> 796 </output>
857 <output name="mqpar" file="06/mqpar.xml" lines_diff="6"> 797 <output name="mqpar" file="06/mqpar.xml" lines_diff="6">
934 <param name="dry_run" value="True" /> 874 <param name="dry_run" value="True" />
935 <param name="output" value="config,mqpar" /> 875 <param name="output" value="config,mqpar" />
936 <output name="config" file="04/config.yml" lines_diff="2" /> 876 <output name="config" file="04/config.yml" lines_diff="2" />
937 <output name="mqpar" file="04/mqpar.xml" lines_diff="12" /> 877 <output name="mqpar" file="04/mqpar.xml" lines_diff="12" />
938 </test> 878 </test>
879 <!-- PTXQC Test -->
880 <test expect_num_outputs="3">
881 <param name="ftype" value=".mzxml" />
882 <param name="fasta_files" value="ptxqc.fasta" />
883 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
884 <param name="description_parse_rule" value="&gt;(.*)" />
885 <repeat name="paramGroups">
886 <param name="files" value="ptxqc.mzXML"/>
887 <param name="variableModifications" value="Oxidation (M)" />
888 <param name="fixedModifications" value="" />
889 <conditional name="quant_method">
890 <param name="select_quant_method" value="reporter_ion_ms2" />
891 <conditional name="iso_labels">
892 <param name="labeling" value="tmt10plex" />
893 </conditional>
894 </conditional>
895 </repeat>
896 <param name="do_it" value="True" />
897 <param name="output" value="config,mqpar" />
898 <output name="config" file="07/config.yml" lines_diff="2" />
899 <!-- high difference due to unconsistant xml formatting in MQ -->
900 <output name="mqpar" file="07/mqpar.xml" lines_diff="24" />
901 <output name="ptxqc_report" file="07/combined/txt/report_v1.0.9_combined.pdf" compare="sim_size" />
902 </test>
939 </tests> 903 </tests>
940 904
941 <help><![CDATA[ 905 <help><![CDATA[
942 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. 906 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
943 907