Mercurial > repos > galaxyp > maxquant
diff maxquant.xml @ 12:0839f84def5e draft
"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 |
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--- a/maxquant.xml Tue Jun 15 07:55:59 2021 +0000 +++ b/maxquant.xml Sun Jun 20 16:37:41 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy5"> +<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy@VERSION_SUFFIX@"> <macros> <xml name="output" token_format="tabular" token_label="default description" token_name="default"> <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> @@ -16,6 +16,13 @@ <command detect_errors="exit_code"><![CDATA[ #import re maxquant -c mqpar.xml 2>/dev/null ## MQ writes success of creation to stderr + + ## Workaround for wrong MQ version in MaxQuantCmd.exe created mqpar.xml (1.6.5.0 instead of 1.6.17.0) + ## Should be removed as soon as MQ is updated with a fixed version + && + sed -i -E 's:(maxQuantVersion>)1.6.5.0(<):\1'1.6.17.0'\2:' mqpar.xml + ## ============================================================================================== + #if 'config' in $output_opts.output: && cp '$mq_conf' '$config' @@ -155,7 +162,7 @@ #end if #if $pg.quant_method.select_quant_method == 'lfq': lfqMode: 1 - lfqSkipNorm: ${pg.quant_method.lfqSkipNorm} + lfqNormType: ${pg.quant_method.lfqNormType} lfqMinEdgesPerNode: ${pg.quant_method.lfqMinEdgesPerNode} lfqAvEdgesPerNode: ${pg.quant_method.lfqAvEdgesPerNode} lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount} @@ -192,6 +199,9 @@ #if $pg.quant_method.iso_labels.labeling == 'tmt11plex': @TMT11PLEX@ #end if + #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex': + @TMTPRO16PLEX@ + #end if #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': @ITRAQ4PLEX@ #end if @@ -234,6 +244,9 @@ #if $pg.quant_method.iso_labels.labeling == 'tmt11plex': @TMT11PLEX@ #end if + #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex': + @TMTPRO16PLEX@ + #end if #if $pg.quant_method.iso_labels.labeling == 'itraq4plex': @ITRAQ4PLEX@ #end if @@ -477,10 +490,11 @@ <param type="integer" name="lfqAvEdgesPerNode" label="LFQ average number of neighbours" value="6" help="Defines the network to normalize the samples in the fast LFQ mode."/> - <param type="boolean" name="lfqSkipNorm" checked="true" - label="Skip normalization" - truevalue="True" falsevalue="False" - 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."/> + <param name="lfqNormType" type="select" label="Normalization type" + multiple="false" help=""> + <option value="0">None</option> + <option value="1">Classic</option> + </param> </when> <when value="reporter_ion_ms2"> <conditional name="iso_labels"> @@ -492,6 +506,7 @@ <option value="tmt8plex">TMT8plex</option> <option value="tmt10plex">TMT10plex</option> <option value="tmt11plex">TMT11plex</option> + <option value="tmtpro16plex">TMTpro16plex</option> <option value="itraq4plex">iTRAQ4plex</option> <option value="itraq8plex">iTRAQ8plex</option> <option value="iodotmt6plex">iodoTMT6plex</option> @@ -501,6 +516,7 @@ <when value="tmt8plex"/> <when value="tmt10plex"/> <when value="tmt11plex"/> + <when value="tmtpro16plex"/> <when value="itraq4plex"/> <when value="itraq8plex"/> <when value="iodotmt6plex"/> @@ -545,6 +561,7 @@ <option value="tmt8plex">TMT8plex</option> <option value="tmt10plex">TMT10plex</option> <option value="tmt11plex">TMT11plex</option> + <option value="tmtpro16plex">TMTpro16plex</option> <option value="itraq4plex">iTRAQ4plex</option> <option value="itraq8plex">iTRAQ8plex</option> <option value="iodotmt6plex">iodoTMT6plex</option> @@ -554,6 +571,7 @@ <when value="tmt8plex"/> <when value="tmt10plex"/> <when value="tmt11plex"/> + <when value="tmtpro16plex"/> <when value="itraq4plex"/> <when value="itraq8plex"/> <when value="iodotmt6plex"/> @@ -643,8 +661,8 @@ <output name="mqpar" file="01/mqpar.xml" lines_diff="6"/> <output name="evidence" file="01/combined/txt/evidence.txt" /> <output name="msms" file="01/combined/txt/msms.txt" /> - <output name="mzTab" file="01/combined/txt/mzTab.mzTab" lines_diff="4"/> - <output name="allPeptides" file="01/combined/txt/allPeptides.txt" lines_diff="4"/> + <output name="mzTab" file="01/combined/txt/mzTab.mzTab" lines_diff="34"/> + <output name="allPeptides" file="01/combined/txt/allPeptides.txt" lines_diff="2"/> <output name="msmsScans" file="01/combined/txt/msmsScans.txt" lines_diff="8"/> <output name="mzRange" file="01/combined/txt/mzRange.txt" /> <output name="parameters" file="01/combined/txt/parameters.txt" lines_diff="10"/> @@ -879,11 +897,11 @@ <!-- PTXQC Test --> <test expect_num_outputs="3"> <param name="ftype" value=".mzxml" /> - <param name="fasta_files" value="ptxqc.fasta" /> + <param name="fasta_files" value="tmt_data.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="files" value="tmt_data.mzXML"/> <param name="variableModifications" value="Oxidation (M)" /> <param name="fixedModifications" value="" /> <conditional name="quant_method"> @@ -897,8 +915,32 @@ <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" /> + <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 --> + <test expect_num_outputs="3"> + <param name="ftype" value=".mzxml" /> + <param name="fasta_files" value="tmt_data_16.fasta" /> + <param name="identifier_parse_rule" value=">([^\s]*)" /> + <param name="description_parse_rule" value=">(.*)" /> + <repeat name="paramGroups"> + <param name="files" value="tmt_data.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="tmtpro16plex" /> + </conditional> + </conditional> + </repeat> + <param name="do_it" value="False" /> + <param name="output" value="config,mqpar,proteinGroups" /> + <output name="config" file="08/config.yml" lines_diff="2" /> + <!-- high difference due to unconsistant xml formatting in MQ --> + <output name="mqpar" file="08/mqpar.xml" lines_diff="24" /> + <output name="proteinGroups" file="08/combined/txt/proteinGroups.txt" /> </test> </tests>