# HG changeset patch
# User galaxyp
# Date 1668366610 0
# Node ID acb5398670861c9ad705a66af24d916bd46f470b
# Parent  6bb7ba55867a0f05063bfdb67c3dc95e8f76c487
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 9d6014f26ea5d3737320ec56749207e6fe602025

diff -r 6bb7ba55867a -r acb539867086 macros.xml
--- a/macros.xml	Mon Jul 25 17:36:06 2022 +0000
+++ b/macros.xml	Sun Nov 13 19:10:10 2022 +0000
@@ -1,8 +1,8 @@
 <?xml version="1.0" ?>
 <macros>
     <token name="@VERSION@">1.6.17.0</token>
-    <token name="@VERSION_SUFFIX@">4</token>
-    <token name="@VERSION_SUFFIX_MQPAR@">0</token>
+    <token name="@VERSION_SUFFIX@">5</token>
+    <token name="@VERSION_SUFFIX_MQPAR@">1</token>
     <token name="@VERSION_PTXQC@">1.0.10</token>
     <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
     <token name="@TMT2PLEX@">
diff -r 6bb7ba55867a -r acb539867086 maxquant.xml
--- a/maxquant.xml	Mon Jul 25 17:36:06 2022 +0000
+++ b/maxquant.xml	Sun Nov 13 19:10:10 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <macros>
         <xml name="output" token_format="tabular" token_label="default description" token_name="default">
             <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
@@ -15,6 +15,8 @@
     <expand macro="requirements"/>
     <expand macro="required_files"/>
     <command detect_errors="exit_code"><![CDATA[
+    ## this is needed to avoid dotnet from crashing, in a newer dotnet version we can remove that
+    export COMPlus_EnableDiagnostics=0 &&
     #import re
     maxquant -c mqpar.xml 2>/dev/null  ## MQ writes success of creation to stderr
 
diff -r 6bb7ba55867a -r acb539867086 maxquant_mqpar.xml
--- a/maxquant_mqpar.xml	Mon Jul 25 17:36:06 2022 +0000
+++ b/maxquant_mqpar.xml	Sun Nov 13 19:10:10 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@">
+<tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@" profile="21.05">
     <macros>
         <xml name="output" token_format="tabular" token_label="default description" token_name="default">
             <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
@@ -15,6 +15,7 @@
     <expand macro="requirements"/>
     <expand macro="required_files"/>
     <command detect_errors="exit_code"><![CDATA[
+    export COMPlus_EnableDiagnostics=0 &&
     ## link galaxy datasets to filenames accepted by maxquant
     #import re
     #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $input_opts.infiles]
@@ -68,8 +69,8 @@
         <conditional name="input_opts">
             <param name="ftype" type="select" label="choose the type of your input files">
                 <option value=".thermo.raw">thermo.raw</option>
-                <option value=".mzxml">mzXML</option>
-                <option value=".mzml">mzML</option>
+                <option value=".mzxml">mzxml</option>
+                <option value=".mzml">mzml</option>
             </param>
             <when value=".thermo.raw"> 
                 <param multiple="true" name="infiles" type="data"
@@ -78,12 +79,12 @@
             </when>
             <when value=".mzxml">
                 <param multiple="true" name="infiles" type="data"
-                       format="mzXML" label="mzXML Files"
+                       format="mzxml" label="mzXML Files"
                        help="Specify one or more mzXML files" />
             </when>
             <when value=".mzml">
                 <param multiple="true" name="infiles" type="data"
-                       format="mzML" label="mzML Files"
+                       format="mzml" label="mzML Files"
                        help="Specify one or more mzML files" />
             </when>
         </conditional>
@@ -193,7 +194,7 @@
 **Input files**
 
 - Thermo raw file or mzXML file
-    - The datatype has to be 'thermo.raw' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
+    - The datatype has to be 'thermo.raw' or 'mzxml'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
 - mqpar.xml: 
     - MaxQuant parameters will be taken from the provided mqpar.xml file. This parameter file MUST be created using the same version of MaxQuant as is used by this tool. The correct version of MaxQuant can be obtained via the bioconda channel for the conda package manager.