Mercurial > repos > galaxyp > maxquant
diff maxquant.xml @ 14:1a3782e58489 draft
"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 |
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--- a/maxquant.xml Thu Jul 08 22:44:53 2021 +0000 +++ b/maxquant.xml Wed Aug 11 09:23:24 2021 +0000 @@ -206,6 +206,9 @@ #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex': @TMTPRO16PLEX@ #end if + #if $pg.quant_method.iso_labels.labeling == 'tmtpro18plex': + @TMTPRO18PLEX@ + #end if #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': @ITRAQ4PLEX@ #end if @@ -251,6 +254,9 @@ #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex': @TMTPRO16PLEX@ #end if + #if $pg.quant_method.iso_labels.labeling == 'tmtpro18plex': + @TMTPRO18PLEX@ + #end if #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': @ITRAQ4PLEX@ #end if @@ -510,6 +516,7 @@ <option value="tmt10plex">TMT10plex</option> <option value="tmt11plex">TMT11plex</option> <option value="tmtpro16plex">TMTpro16plex</option> + <option value="tmtpro18plex">TMTpro18plex</option> <option value="itraq4plex">iTRAQ4plex</option> <option value="itraq8plex">iTRAQ8plex</option> <option value="iodotmt6plex">iodoTMT6plex</option> @@ -520,6 +527,7 @@ <when value="tmt10plex"/> <when value="tmt11plex"/> <when value="tmtpro16plex"/> + <when value="tmtpro18plex"/> <when value="itraq4plex"/> <when value="itraq8plex"/> <when value="iodotmt6plex"/> @@ -565,6 +573,7 @@ <option value="tmt10plex">TMT10plex</option> <option value="tmt11plex">TMT11plex</option> <option value="tmtpro16plex">TMTpro16plex</option> + <option value="tmtpro18plex">TMTpro18plex</option> <option value="itraq4plex">iTRAQ4plex</option> <option value="itraq8plex">iTRAQ8plex</option> <option value="iodotmt6plex">iodoTMT6plex</option> @@ -575,6 +584,7 @@ <when value="tmt10plex"/> <when value="tmt11plex"/> <when value="tmtpro16plex"/> + <when value="tmtpro18plex"/> <when value="itraq4plex"/> <when value="itraq8plex"/> <when value="iodotmt6plex"/> @@ -921,7 +931,7 @@ <output name="mqpar" file="07/mqpar.xml" lines_diff="4" /> <output name="ptxqc_report" file="07/combined/txt/report_v1.0.10_combined.pdf" compare="sim_size" /> </test> - <!-- TMTpro16plex test --> + <!-- TMTpro16plex test --> <test expect_num_outputs="3"> <param name="ftype" value=".mzxml" /> <param name="fasta_files" value="tmt_data_16.fasta" /> @@ -945,6 +955,50 @@ <output name="mqpar" file="08/mqpar.xml" lines_diff="24" /> <output name="proteinGroups" file="08/combined/txt/proteinGroups.txt" /> </test> + <!-- TMTpro18plex test --> + <test expect_num_outputs="2"> + <param name="ftype" value=".mzxml" /> + <param name="fasta_files" value="tmt_data_18.fasta" /> + <param name="identifier_parse_rule" value=">([^\s]*)" /> + <param name="description_parse_rule" value=">(.*)" /> + <repeat name="paramGroups"> + <param name="files" value="tmt_data_18.mzXML"/> + <param name="variableModifications" value="Oxidation (M)" /> + <param name="fixedModifications" value="" /> + <conditional name="quant_method"> + <param name="select_quant_method" value="reporter_ion_ms2" /> + <conditional name="iso_labels"> + <param name="labeling" value="tmtpro18plex" /> + </conditional> + </conditional> + </repeat> + <param name="do_it" value="False" /> + <param name="output" value="msmsScans" /> + <output name="msmsScans" file="09/combined/txt/msmsScans.txt"> + <assert_contents> + <has_text text="GANDSMMM" /> + </assert_contents> + </output> + </test> + <!-- Thermo RAW file test --> + <test expect_num_outputs="2"> + <param name="ftype" value=".thermo.raw" /> + <param name="fasta_files" value="bsa.fasta" /> + <param name="identifier_parse_rule" value="^>.*\|(.*)\|.*$" /> + <param name="description_parse_rule" value="^>.*\|.*\|[^ ]+ (.*) OS.*$" /> + <param name="min_unique_pep" value="1" /> + <repeat name="paramGroups"> + <param name="files" value="thermo.raw"/> + <param name="maxMissedCleavages" value="1"/> + <param name="variableModifications" value="Oxidation (M)" /> + <conditional name="quant_method"> + <param name="select_quant_method" value="lfq" /> + </conditional> + </repeat> + <param name="output" value="config,mqpar" /> + <output name="config" file="10/config.yml" lines_diff="2" /> + <output name="mqpar" file="10/mqpar.xml" lines_diff="10" /> + </test> </tests> <help><![CDATA[ @@ -980,7 +1034,7 @@ - Tabular file with experimental design template: - - 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: + - 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: :: @@ -1003,6 +1057,18 @@ File4 1 (missing experiment) (File5 missing) + - However, “.raw” (Thermo) is considered a part of the filename: + + :: + + Name Fraction Experiment PTM + File1.raw 1 E1 False + File2.raw 2 E1 False + File3.raw 3 E1 False + File4.raw 1 E2 False + File5.raw 2 E2 False + File6.raw 3 E2 False + **Parameter Options** - Quantitation methods (in section parameter groups)