# HG changeset patch
# User galaxyp
# Date 1675188833 0
# Node ID 5879e0825ce66d9f064607bf198a22a7e2772b73
# Parent  717b3d7014328ea42bcd49fb6be00ad1aca2fc6d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 86de2cd327423c44d042f98108dc93a8f83982d0

diff -r 717b3d701432 -r 5879e0825ce6 msstats.xml
--- a/msstats.xml	Fri Aug 06 20:05:40 2021 +0000
+++ b/msstats.xml	Tue Jan 31 18:13:53 2023 +0000
@@ -1,7 +1,8 @@
-<tool id="msstats" name="MSstats" version="@VERSION@.0">
+<tool id="msstats" name="MSstats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry</description>
     <macros>
-        <token name="@VERSION@">4.0.0</token>
+        <token name="@TOOL_VERSION@">4.0.0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <xml name="useUniquePeptide">
             <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove peptides that are assigned for more than one proteins"/>
         </xml>
@@ -23,7 +24,7 @@
         
     </macros>
     <requirements>
-        <requirement type="package" version="@VERSION@">bioconductor-msstats</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-msstats</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         cat '$msstats_script' > '$r_script' &&
@@ -1013,7 +1014,7 @@
     <help><![CDATA[
 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/>`_
 
-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. 
+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.
 
 -----
 
@@ -1229,6 +1230,7 @@
     ]]></help>
     <citations>
         <citation type="doi">10.1093/bioinformatics/btu305</citation>
+        <citation type="doi">10.1021/acs.jproteome.2c00051</citation>
     </citations>
 </tool>