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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 86de2cd327423c44d042f98108dc93a8f83982d0
author galaxyp
date Tue, 31 Jan 2023 18:13:53 +0000
parents 717b3d701432
children
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5:717b3d701432 6:5879e0825ce6
1 <tool id="msstats" name="MSstats" version="@VERSION@.0"> 1 <tool id="msstats" name="MSstats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry</description> 2 <description>statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">4.0.0</token> 4 <token name="@TOOL_VERSION@">4.0.0</token>
5 <token name="@VERSION_SUFFIX@">1</token>
5 <xml name="useUniquePeptide"> 6 <xml name="useUniquePeptide">
6 <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove peptides that are assigned for more than one proteins"/> 7 <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove peptides that are assigned for more than one proteins"/>
7 </xml> 8 </xml>
8 <xml name="summaryforMultipleRows"> 9 <xml name="summaryforMultipleRows">
9 <param name="summaryforMultipleRows" type="select" label="Summary for MultipleRows" help="When there are multiple measurements for certain feature and certain run, use highest or sum of all"> 10 <param name="summaryforMultipleRows" type="select" label="Summary for MultipleRows" help="When there are multiple measurements for certain feature and certain run, use highest or sum of all">
21 <param name="removeProtein_with1Peptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the proteins which have only 1 peptide and charge"/> 22 <param name="removeProtein_with1Peptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the proteins which have only 1 peptide and charge"/>
22 </xml> 23 </xml>
23 24
24 </macros> 25 </macros>
25 <requirements> 26 <requirements>
26 <requirement type="package" version="@VERSION@">bioconductor-msstats</requirement> 27 <requirement type="package" version="@TOOL_VERSION@">bioconductor-msstats</requirement>
27 </requirements> 28 </requirements>
28 <command detect_errors="exit_code"><![CDATA[ 29 <command detect_errors="exit_code"><![CDATA[
29 cat '$msstats_script' > '$r_script' && 30 cat '$msstats_script' > '$r_script' &&
30 Rscript '$msstats_script' 31 Rscript '$msstats_script'
31 ]]></command> 32 ]]></command>
1011 1012
1012 </tests> 1013 </tests>
1013 <help><![CDATA[ 1014 <help><![CDATA[
1014 MSstats is an open-source R package for statistical relative quantification of proteins and peptides in global, targeted and data-independent proteomics. `More information on MSstats <http://msstats.org/>`_ 1015 MSstats is an open-source R package for statistical relative quantification of proteins and peptides in global, targeted and data-independent proteomics. `More information on MSstats <http://msstats.org/>`_
1015 1016
1016 The MSstats Galaxy tool (version @VERSION@) allows the detection of differentially abundant proteins for label-free MS experiments with complex designs on data derived from open-source proteomics software available in Galaxy (e.g. MaxQuant, OpenMS, OpenSWATH). Processing functionalities such as log transformation, normalization, feature selection, missing value imputation and quantification are available as well. 1017 The MSstats Galaxy tool (version @TOOL_VERSION@) allows the detection of differentially abundant proteins for label-free MS experiments with complex designs on data derived from open-source proteomics software available in Galaxy (e.g. MaxQuant, OpenMS, OpenSWATH). Processing functionalities such as log transformation, normalization, feature selection, missing value imputation and quantification are available as well.
1017 1018
1018 ----- 1019 -----
1019 1020
1020 **Input data** 1021 **Input data**
1021 1022
1227 1228
1228 1229
1229 ]]></help> 1230 ]]></help>
1230 <citations> 1231 <citations>
1231 <citation type="doi">10.1093/bioinformatics/btu305</citation> 1232 <citation type="doi">10.1093/bioinformatics/btu305</citation>
1233 <citation type="doi">10.1021/acs.jproteome.2c00051</citation>
1232 </citations> 1234 </citations>
1233 </tool> 1235 </tool>
1234 1236