Mercurial > repos > galaxyp > maxquant
diff maxquant.xml @ 11:d72c96ad9a16 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
| author | galaxyp |
|---|---|
| date | Tue, 15 Jun 2021 07:55:59 +0000 |
| parents | f522c08e900c |
| children | 0839f84def5e |
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--- a/maxquant.xml Fri Mar 12 08:41:06 2021 +0000 +++ b/maxquant.xml Tue Jun 15 07:55:59 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy4"> +<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy5"> <macros> <xml name="output" token_format="tabular" token_label="default description" token_name="default"> <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> @@ -63,7 +63,7 @@ >> '$log' 2>&1 #end if && - cp ./combined/txt/report_v0.92.6_combined.pdf '$ptxqc_report' + cp './combined/txt/report_v@VERSION_PTXQC@_combined.pdf' '$ptxqc_report' #end if #end if ]]></command> @@ -178,57 +178,28 @@ #end for #end if #if $pg.quant_method.iso_labels.labeling == 'tmt2plex': - - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] - - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True] + @TMT2PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'tmt6plex': - - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True] - - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True] - - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True] - - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True] - - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True] - - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True] + @TMT6PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'tmt8plex': - - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True] - - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True] - - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True] - - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True] - - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True] - - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True] - - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True] - - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True] + @TMT8PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'tmt10plex': @TMT10PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'tmt11plex': - @TMT10PLEX@ - - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True] + @TMT11PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': - - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] - - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] - - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False] - - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False] + @ITRAQ4PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'itraq8plex': - - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False] - - [iTRAQ4plex-Lys114,iTRAQ8plex-Nter114,0,0,0,0,False] - - [iTRAQ4plex-Lys115,iTRAQ8plex-Nter115,0,0,0,0,False] - - [iTRAQ4plex-Lys116,iTRAQ8plex-Nter116,0,0,0,0,False] - - [iTRAQ4plex-Lys117,iTRAQ8plex-Nter117,0,0,0,0,False] - - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False] - - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False] - - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False] + @ITRAQ8PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex': - - [iodoTMT6plex-Cys126,'',0,0,0,0,True] - - [iodoTMT6plex-Cys127,'',0,0,0,0,True] - - [iodoTMT6plex-Cys128,'',0,0,0,0,True] - - [iodoTMT6plex-Cys129,'',0,0,0,0,True] - - [iodoTMT6plex-Cys130,'',0,0,0,0,True] - - [iodoTMT6plex-Cys131,'',0,0,0,0,True] + @IODOTMT6PLEX@ #end if #end if #if $pg.quant_method.select_quant_method == 'reporter_ion_ms3': @@ -248,58 +219,29 @@ - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike] #end for #end if - #if $pg.quant_method.iso_labels.labeling == 'tmt2plex': - - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] - - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True] + #if $pg.quant_method.iso_labels.labeling == 'tmt2plex': + @TMT2PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'tmt6plex': - - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True] - - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True] - - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True] - - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True] - - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True] - - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True] + @TMT6PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'tmt8plex': - - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True] - - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True] - - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True] - - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True] - - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True] - - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True] - - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True] - - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True] + @TMT8PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'tmt10plex': @TMT10PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'tmt11plex': - @TMT10PLEX@ - - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True] + @TMT11PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': - - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] - - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] - - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False] - - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False] + @ITRAQ4PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'itraq8plex': - - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False] - - [iTRAQ4plex-Lys114,iTRAQ8plex-Nter114,0,0,0,0,False] - - [iTRAQ4plex-Lys115,iTRAQ8plex-Nter115,0,0,0,0,False] - - [iTRAQ4plex-Lys116,iTRAQ8plex-Nter116,0,0,0,0,False] - - [iTRAQ4plex-Lys117,iTRAQ8plex-Nter117,0,0,0,0,False] - - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False] - - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False] - - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False] + @ITRAQ8PLEX@ #end if #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex': - - [iodoTMT6plex-Cys126,'',0,0,0,0,True] - - [iodoTMT6plex-Cys127,'',0,0,0,0,True] - - [iodoTMT6plex-Cys128,'',0,0,0,0,True] - - [iodoTMT6plex-Cys129,'',0,0,0,0,True] - - [iodoTMT6plex-Cys130,'',0,0,0,0,True] - - [iodoTMT6plex-Cys131,'',0,0,0,0,True] + @IODOTMT6PLEX@ #end if #end if #end for @@ -554,15 +496,14 @@ <option value="itraq8plex">iTRAQ8plex</option> <option value="iodotmt6plex">iodoTMT6plex</option> </param> - - <when value="tmt2plex"></when> - <when value="tmt6plex"></when> - <when value="tmt8plex"></when> - <when value="tmt10plex"></when> - <when value="tmt11plex"></when> - <when value="itraq4plex"></when> - <when value="itraq8plex"></when> - <when value="iodotmt6plex"></when> + <when value="tmt2plex"/> + <when value="tmt6plex"/> + <when value="tmt8plex"/> + <when value="tmt10plex"/> + <when value="tmt11plex"/> + <when value="itraq4plex"/> + <when value="itraq8plex"/> + <when value="iodotmt6plex"/> <when value="custom"> <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> <param name="internallabel" type="select" label="internal label" help="contains Lys"> @@ -591,7 +532,7 @@ max="1" help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/> </when> - <when value="False"></when> + <when value="False"/> </conditional> </when> <when value="reporter_ion_ms3"> @@ -608,15 +549,14 @@ <option value="itraq8plex">iTRAQ8plex</option> <option value="iodotmt6plex">iodoTMT6plex</option> </param> - - <when value="tmt2plex"></when> - <when value="tmt6plex"></when> - <when value="tmt8plex"></when> - <when value="tmt10plex"></when> - <when value="tmt11plex"></when> - <when value="itraq4plex"></when> - <when value="itraq8plex"></when> - <when value="iodotmt6plex"></when> + <when value="tmt2plex"/> + <when value="tmt6plex"/> + <when value="tmt8plex"/> + <when value="tmt10plex"/> + <when value="tmt11plex"/> + <when value="itraq4plex"/> + <when value="itraq8plex"/> + <when value="iodotmt6plex"/> <when value="custom"> <repeat name="iso_label" title="Isobaric Label" min="1" default="1"> <param name="internallabel" type="select" label="internal label" help="contains Lys"> @@ -645,7 +585,7 @@ max="1" help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/> </when> - <when value="False"></when> + <when value="False"/> </conditional> </when> </conditional> @@ -663,7 +603,7 @@ <option value="mqpar">mqpar.xml</option> <option value="peptides">Peptides</option> <option value="evidence">Evidence</option> - <option value="parameters">Tabular Paramters</option> + <option value="parameters">Tabular Parameters</option> <option value="msms">MSMS</option> <option value="mzTab">mzTab</option> <option value="allPeptides">all peptides</option> @@ -780,7 +720,7 @@ </repeat> <param name="dry_run" value="True" /> <param name="output" value="config,mqpar,mzTab" /> - <output name="config" file="02/config.yml" lines_diff="2" /> + <output name="config" file="02/config.yml" lines_diff="7" /> <!-- high difference due to unconsistant xml formatting in MQ --> <output name="mqpar" file="02/mqpar.xml" lines_diff="24" /> </test> @@ -849,7 +789,7 @@ </repeat> <param name="dry_run" value="True" /> <param name="output" value="config,mqpar,mzTab" /> - <output name="config" file="06/config.yml" lines_diff="2"> + <output name="config" file="06/config.yml" lines_diff="7"> <assert_contents> <has_text_matching expression="lcmsRunType\: \'Reporter ion MS3\'" /> </assert_contents> @@ -936,6 +876,30 @@ <output name="config" file="04/config.yml" lines_diff="2" /> <output name="mqpar" file="04/mqpar.xml" lines_diff="12" /> </test> + <!-- PTXQC Test --> + <test expect_num_outputs="3"> + <param name="ftype" value=".mzxml" /> + <param name="fasta_files" value="ptxqc.fasta" /> + <param name="identifier_parse_rule" value=">([^\s]*)" /> + <param name="description_parse_rule" value=">(.*)" /> + <repeat name="paramGroups"> + <param name="files" value="ptxqc.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="tmt10plex" /> + </conditional> + </conditional> + </repeat> + <param name="do_it" value="True" /> + <param name="output" value="config,mqpar" /> + <output name="config" file="07/config.yml" lines_diff="2" /> + <!-- high difference due to unconsistant xml formatting in MQ --> + <output name="mqpar" file="07/mqpar.xml" lines_diff="24" /> + <output name="ptxqc_report" file="07/combined/txt/report_v1.0.9_combined.pdf" compare="sim_size" /> + </test> </tests> <help><![CDATA[