maxquant: macros.xml comparison

comparison macros.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

comparison

equal deleted inserted replaced

-:f522c08e900c
+:d72c96ad9a16
 <?xml version="1.0" ?>
 <macros>
 <token name="@VERSION@">1.6.10.43</token>
+<token name="@VERSION_PTXQC@">1.0.9</token>
 <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
-<token name="@TMT10PLEX@"><![CDATA[- [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True]
+<token name="@TMT2PLEX@">
+- [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
+- [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]
+</token>
+<token name="@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]
+</token>
+<token name="@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]
+</token>
+<token name="@TMT10PLEX@">
+- [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True]
 - [TMT10plex-Lys127N,TMT10plex-Nter127N,0,0,0,0,True]
 - [TMT10plex-Lys127C,TMT10plex-Nter127C,0,0,0,0,True]
 - [TMT10plex-Lys128N,TMT10plex-Nter128N,0,0,0,0,True]
 - [TMT10plex-Lys128C,TMT10plex-Nter128C,0,0,0,0,True]
 - [TMT10plex-Lys129N,TMT10plex-Nter129N,0,0,0,0,True]
 - [TMT10plex-Lys129C,TMT10plex-Nter129C,0,0,0,0,True]
 - [TMT10plex-Lys130N,TMT10plex-Nter130N,0,0,0,0,True]
 - [TMT10plex-Lys130C,TMT10plex-Nter130C,0,0,0,0,True]
 - [TMT10plex-Lys131N,TMT10plex-Nter131N,0,0,0,0,True]
-]]></token>
+</token>
+<token name="@TMT11PLEX@">
+@TMT10PLEX@
+- [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True]
+</token>
+<token name="@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]
+</token>
+<token name="@ITRAQ8PLEX@">
+- [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False]
+@ITRAQ4PLEX@
+- [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]
+</token>
+<token name="@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]
+</token>
 <xml name="requirements">
 <requirements>
 <requirement type="package" version="@VERSION@">maxquant</requirement>
 <requirement type="package" version="3.7">python</requirement>
 <requirement type="package" version="5.1.2">pyyaml</requirement>
-<requirement type="package" version="0.92.6">r-ptxqc</requirement>
+<requirement type="package" version="@VERSION_PTXQC@">r-ptxqc</requirement>
 <requirement type="package" version="1.32">tar</requirement>
 </requirements>
 </xml>
 <xml name="ptxqc">
 <configfile name="qr_yaml">
 PTXQC:
 ReportFilename:
 extended: yes
 qcMetric_EVD_ProteinCount: 450.0
 qcMetric_AverageQualOverall: 9999.0
 </configfile>
 <configfile name="qr">
 library(PTXQC)
+library(data.table)
 library(yaml)
 library(methods)
 args = commandArgs(trailingOnly=TRUE)
 yaml_config = yaml.load_file(input = args[1])
-r = createReport('./combined/txt', yaml_config)
+r = createReport('./combined/txt', yaml_obj=yaml_config)
 cat(paste0("\nReport generated as '", r\$report_file, "'\n\n"))
 </configfile>
 </xml>
 <xml name="mod_option" token_value="default">
 <option value="@VALUE@">@VALUE@</option>
 </xml>
 <xml name="default_mod_option" token_value="default">
 <option selected="true" value="@VALUE@">@VALUE@</option>
 </xml>
 <xml name="ptxqc-opts">
 <conditional name="qc">
-<param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)"
+<param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" type="boolean" checked="false"/>
-type="boolean" checked="false"/>
 <when value="true">
-<param name="parameters" type="boolean" checked="true"
+<param name="parameters" type="boolean" checked="true" label="use parameters.txt?" truevalue="yes" falsevalue="no"/>
-	               label="use parameters.txt?" truevalue="yes" falsevalue="no" />
+<param name="summary" type="boolean" checked="true" label="use summary.txt?" truevalue="yes" falsevalue="no"/>
-<param name="summary" type="boolean" checked="true"
+<param name="proteingroups" type="boolean" checked="true" label="use proteinGroups.txt?" truevalue="yes" falsevalue="no"/>
-	               label="use summary.txt?" truevalue="yes" falsevalue="no" />
+<param name="evidence" type="boolean" checked="true" label="use evidence.txt?" truevalue="yes" falsevalue="no"/>
-<param name="proteingroups" type="boolean" checked="true"
+<param name="msms" type="boolean" checked="true" label="use msms.txt?" truevalue="yes" falsevalue="no"/>
-	               label="use proteinGroups.txt?" truevalue="yes" falsevalue="no" />
+<param name="msmsscans" type="boolean" checked="true" label="use msmsScans.txt?" truevalue="yes" falsevalue="no"/>
-<param name="evidence" type="boolean" checked="true"
-	               label="use evidence.txt?" truevalue="yes" falsevalue="no" />
-<param name="msms" type="boolean" checked="true"
-	               label="use msms.txt?" truevalue="yes" falsevalue="no" />
-<param name="msmsscans" type="boolean" checked="true"
-	               label="use msmsScans.txt?" truevalue="yes" falsevalue="no" />
 </when>
 <when value="false"/>
 </conditional>
 </xml>
 <xml name="outputs">
 <outputs>
 <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/>
 <expand macro="output_from_wdir" name="mqpar" label="mqpar.xml" format="xml" ext="xml"/>
 <expand macro="output_from_wdir" name="peptides" label="MaxQuant Peptides"/>
 <data format="pdf" label="PTXQC report for ${on_string}" name="ptxqc_report">
 <filter>qc['do_it'] == True</filter>
 </data>
 </outputs>
 </xml>
 <xml name="modification">
 <expand macro="mod_option" value="Acetyl (K)"/>
 <expand macro="mod_option" value="Acetyl (Protein N-term)"/>
 <expand macro="mod_option" value="Carbamidomethyl (C)"/>
 <expand macro="mod_option" value="Oxidation (M)"/>
 <expand macro="mod_option" value="Val-&gt;CamCys"/>
 <expand macro="mod_option" value="Xle-&gt;CamCys"/>
 <expand macro="mod_option" value="Cysteinyl"/>
 <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/>
 </xml>
 <xml name="label">
 <expand macro="mod_option" value="Arg6"/>
 <expand macro="mod_option" value="Arg10"/>
 <expand macro="mod_option" value="Lys4"/>
 <expand macro="mod_option" value="Lys6"/>
 <expand macro="mod_option" value="DimethLys6"/>
 <expand macro="mod_option" value="DimethNter6"/>
 <expand macro="mod_option" value="Leu7"/>
 <expand macro="mod_option" value="Ile7"/>
 </xml>
 <xml name="proteases">
 <expand macro="mod_option" value="Trypsin"/>
 <expand macro="mod_option" value="Trypsin/P"/>
 <expand macro="mod_option" value="LysC"/>
 <expand macro="mod_option" value="LysC/P"/>
 <expand macro="mod_option" value="AspN"/>
 <expand macro="mod_option" value="LysN"/>
 <expand macro="mod_option" value="Chymotrypsin+"/>
 <expand macro="mod_option" value="Chymotrypsin"/>
 </xml>
 <xml name="iso_labels">
 <expand macro="mod_option" value="iTRAQ4plex-Nter114"/>
 <expand macro="mod_option" value="iTRAQ4plex-Nter115"/>
 <expand macro="mod_option" value="iTRAQ4plex-Nter116"/>
 <expand macro="mod_option" value="iTRAQ4plex-Nter117"/>
 <expand macro="mod_option" value="iodoTMT6plex-Cys128"/>
 <expand macro="mod_option" value="iodoTMT6plex-Cys129"/>
 <expand macro="mod_option" value="iodoTMT6plex-Cys130"/>
 <expand macro="mod_option" value="iodoTMT6plex-Cys131"/>
 </xml>
+<xml name="citations">
-<xml name="citations">
 <citations>
 <citation type="bibtex">
 @article{cox2008maxquant,
 title={MaxQuant enables high peptide identification rates, individualized
 ppb-range mass accuracies and proteome-wide protein quantification},

Mercurial > repos > galaxyp > maxquant

comparison macros.xml @ 11:d72c96ad9a16 draft