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comparison maxquant.xml @ 14:1a3782e58489 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
author galaxyp
date Wed, 11 Aug 2021 09:23:24 +0000
parents 63b1c8b6192b
children 41a49d4b2bc3
comparison
equal deleted inserted replaced
13:63b1c8b6192b 14:1a3782e58489
204 @TMT11PLEX@ 204 @TMT11PLEX@
205 #end if 205 #end if
206 #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex': 206 #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex':
207 @TMTPRO16PLEX@ 207 @TMTPRO16PLEX@
208 #end if 208 #end if
209 #if $pg.quant_method.iso_labels.labeling == 'tmtpro18plex':
210 @TMTPRO18PLEX@
211 #end if
209 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': 212 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex':
210 @ITRAQ4PLEX@ 213 @ITRAQ4PLEX@
211 #end if 214 #end if
212 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex': 215 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex':
213 @ITRAQ8PLEX@ 216 @ITRAQ8PLEX@
248 #if $pg.quant_method.iso_labels.labeling == 'tmt11plex': 251 #if $pg.quant_method.iso_labels.labeling == 'tmt11plex':
249 @TMT11PLEX@ 252 @TMT11PLEX@
250 #end if 253 #end if
251 #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex': 254 #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex':
252 @TMTPRO16PLEX@ 255 @TMTPRO16PLEX@
256 #end if
257 #if $pg.quant_method.iso_labels.labeling == 'tmtpro18plex':
258 @TMTPRO18PLEX@
253 #end if 259 #end if
254 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': 260 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex':
255 @ITRAQ4PLEX@ 261 @ITRAQ4PLEX@
256 #end if 262 #end if
257 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex': 263 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex':
508 <option value="tmt6plex">TMT6plex</option> 514 <option value="tmt6plex">TMT6plex</option>
509 <option value="tmt8plex">TMT8plex</option> 515 <option value="tmt8plex">TMT8plex</option>
510 <option value="tmt10plex">TMT10plex</option> 516 <option value="tmt10plex">TMT10plex</option>
511 <option value="tmt11plex">TMT11plex</option> 517 <option value="tmt11plex">TMT11plex</option>
512 <option value="tmtpro16plex">TMTpro16plex</option> 518 <option value="tmtpro16plex">TMTpro16plex</option>
519 <option value="tmtpro18plex">TMTpro18plex</option>
513 <option value="itraq4plex">iTRAQ4plex</option> 520 <option value="itraq4plex">iTRAQ4plex</option>
514 <option value="itraq8plex">iTRAQ8plex</option> 521 <option value="itraq8plex">iTRAQ8plex</option>
515 <option value="iodotmt6plex">iodoTMT6plex</option> 522 <option value="iodotmt6plex">iodoTMT6plex</option>
516 </param> 523 </param>
517 <when value="tmt2plex"/> 524 <when value="tmt2plex"/>
518 <when value="tmt6plex"/> 525 <when value="tmt6plex"/>
519 <when value="tmt8plex"/> 526 <when value="tmt8plex"/>
520 <when value="tmt10plex"/> 527 <when value="tmt10plex"/>
521 <when value="tmt11plex"/> 528 <when value="tmt11plex"/>
522 <when value="tmtpro16plex"/> 529 <when value="tmtpro16plex"/>
530 <when value="tmtpro18plex"/>
523 <when value="itraq4plex"/> 531 <when value="itraq4plex"/>
524 <when value="itraq8plex"/> 532 <when value="itraq8plex"/>
525 <when value="iodotmt6plex"/> 533 <when value="iodotmt6plex"/>
526 <when value="custom"> 534 <when value="custom">
527 <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> 535 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
563 <option value="tmt6plex">TMT6plex</option> 571 <option value="tmt6plex">TMT6plex</option>
564 <option value="tmt8plex">TMT8plex</option> 572 <option value="tmt8plex">TMT8plex</option>
565 <option value="tmt10plex">TMT10plex</option> 573 <option value="tmt10plex">TMT10plex</option>
566 <option value="tmt11plex">TMT11plex</option> 574 <option value="tmt11plex">TMT11plex</option>
567 <option value="tmtpro16plex">TMTpro16plex</option> 575 <option value="tmtpro16plex">TMTpro16plex</option>
576 <option value="tmtpro18plex">TMTpro18plex</option>
568 <option value="itraq4plex">iTRAQ4plex</option> 577 <option value="itraq4plex">iTRAQ4plex</option>
569 <option value="itraq8plex">iTRAQ8plex</option> 578 <option value="itraq8plex">iTRAQ8plex</option>
570 <option value="iodotmt6plex">iodoTMT6plex</option> 579 <option value="iodotmt6plex">iodoTMT6plex</option>
571 </param> 580 </param>
572 <when value="tmt2plex"/> 581 <when value="tmt2plex"/>
573 <when value="tmt6plex"/> 582 <when value="tmt6plex"/>
574 <when value="tmt8plex"/> 583 <when value="tmt8plex"/>
575 <when value="tmt10plex"/> 584 <when value="tmt10plex"/>
576 <when value="tmt11plex"/> 585 <when value="tmt11plex"/>
577 <when value="tmtpro16plex"/> 586 <when value="tmtpro16plex"/>
587 <when value="tmtpro18plex"/>
578 <when value="itraq4plex"/> 588 <when value="itraq4plex"/>
579 <when value="itraq8plex"/> 589 <when value="itraq8plex"/>
580 <when value="iodotmt6plex"/> 590 <when value="iodotmt6plex"/>
581 <when value="custom"> 591 <when value="custom">
582 <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> 592 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
919 <output name="config" file="07/config.yml" lines_diff="2" /> 929 <output name="config" file="07/config.yml" lines_diff="2" />
920 <!-- high difference due to unconsistant xml formatting in MQ --> 930 <!-- high difference due to unconsistant xml formatting in MQ -->
921 <output name="mqpar" file="07/mqpar.xml" lines_diff="4" /> 931 <output name="mqpar" file="07/mqpar.xml" lines_diff="4" />
922 <output name="ptxqc_report" file="07/combined/txt/report_v1.0.10_combined.pdf" compare="sim_size" /> 932 <output name="ptxqc_report" file="07/combined/txt/report_v1.0.10_combined.pdf" compare="sim_size" />
923 </test> 933 </test>
924 <!-- TMTpro16plex test --> 934 <!-- TMTpro16plex test -->
925 <test expect_num_outputs="3"> 935 <test expect_num_outputs="3">
926 <param name="ftype" value=".mzxml" /> 936 <param name="ftype" value=".mzxml" />
927 <param name="fasta_files" value="tmt_data_16.fasta" /> 937 <param name="fasta_files" value="tmt_data_16.fasta" />
928 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 938 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
929 <param name="description_parse_rule" value="&gt;(.*)" /> 939 <param name="description_parse_rule" value="&gt;(.*)" />
943 <output name="config" file="08/config.yml" lines_diff="2" /> 953 <output name="config" file="08/config.yml" lines_diff="2" />
944 <!-- high difference due to unconsistant xml formatting in MQ --> 954 <!-- high difference due to unconsistant xml formatting in MQ -->
945 <output name="mqpar" file="08/mqpar.xml" lines_diff="24" /> 955 <output name="mqpar" file="08/mqpar.xml" lines_diff="24" />
946 <output name="proteinGroups" file="08/combined/txt/proteinGroups.txt" /> 956 <output name="proteinGroups" file="08/combined/txt/proteinGroups.txt" />
947 </test> 957 </test>
958 <!-- TMTpro18plex test -->
959 <test expect_num_outputs="2">
960 <param name="ftype" value=".mzxml" />
961 <param name="fasta_files" value="tmt_data_18.fasta" />
962 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
963 <param name="description_parse_rule" value="&gt;(.*)" />
964 <repeat name="paramGroups">
965 <param name="files" value="tmt_data_18.mzXML"/>
966 <param name="variableModifications" value="Oxidation (M)" />
967 <param name="fixedModifications" value="" />
968 <conditional name="quant_method">
969 <param name="select_quant_method" value="reporter_ion_ms2" />
970 <conditional name="iso_labels">
971 <param name="labeling" value="tmtpro18plex" />
972 </conditional>
973 </conditional>
974 </repeat>
975 <param name="do_it" value="False" />
976 <param name="output" value="msmsScans" />
977 <output name="msmsScans" file="09/combined/txt/msmsScans.txt">
978 <assert_contents>
979 <has_text text="GANDSMMM" />
980 </assert_contents>
981 </output>
982 </test>
983 <!-- Thermo RAW file test -->
984 <test expect_num_outputs="2">
985 <param name="ftype" value=".thermo.raw" />
986 <param name="fasta_files" value="bsa.fasta" />
987 <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" />
988 <param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" />
989 <param name="min_unique_pep" value="1" />
990 <repeat name="paramGroups">
991 <param name="files" value="thermo.raw"/>
992 <param name="maxMissedCleavages" value="1"/>
993 <param name="variableModifications" value="Oxidation (M)" />
994 <conditional name="quant_method">
995 <param name="select_quant_method" value="lfq" />
996 </conditional>
997 </repeat>
998 <param name="output" value="config,mqpar" />
999 <output name="config" file="10/config.yml" lines_diff="2" />
1000 <output name="mqpar" file="10/mqpar.xml" lines_diff="10" />
1001 </test>
948 </tests> 1002 </tests>
949 1003
950 <help><![CDATA[ 1004 <help><![CDATA[
951 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. 1005 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
952 1006
978 1032
979 - Optional files: 1033 - Optional files:
980 1034
981 - Tabular file with experimental design template: 1035 - Tabular file with experimental design template:
982 1036
983 - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Experiment are abitrary strings, Fraction is an integer or emtpy, PTM is either 'True', 'False' or empty. Consider you uploaded files named File1.mzxml, ..., File5.mzxml. This is a (syntactically) correct experimental design template: 1037 - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Experiment are abitrary strings, Fraction is an integer or emtpy, PTM is either 'True', 'False' or empty. Consider you uploaded files named File1.mzxml, ..., File5.mzxml. Thermo RAW files are handled differently (see table below). This is a (syntactically) correct experimental design template:
984 1038
985 :: 1039 ::
986 1040
987 Name Fraction Experiment PTM 1041 Name Fraction Experiment PTM
988 File1 1 E1 False 1042 File1 1 E1 False
1001 File2.mzxml 1 E2 (filename with extension) 1055 File2.mzxml 1 E2 (filename with extension)
1002 File3 f3 E1 (fraction not an integer) 1056 File3 f3 E1 (fraction not an integer)
1003 File4 1 (missing experiment) 1057 File4 1 (missing experiment)
1004 (File5 missing) 1058 (File5 missing)
1005 1059
1060 - However, “.raw” (Thermo) is considered a part of the filename:
1061
1062 ::
1063
1064 Name Fraction Experiment PTM
1065 File1.raw 1 E1 False
1066 File2.raw 2 E1 False
1067 File3.raw 3 E1 False
1068 File4.raw 1 E2 False
1069 File5.raw 2 E2 False
1070 File6.raw 3 E2 False
1071
1006 **Parameter Options** 1072 **Parameter Options**
1007 1073
1008 - Quantitation methods (in section parameter groups) 1074 - Quantitation methods (in section parameter groups)
1009 1075
1010 - label free (LFQ): Protein intensity will be reported as 'LFQ intensity' columns in the proteinGroups table 1076 - label free (LFQ): Protein intensity will be reported as 'LFQ intensity' columns in the proteinGroups table