# HG changeset patch
# User galaxyp
# Date 1658473770 0
# Node ID 41a49d4b2bc3c75a465dc12abad9198947fc5d2d
# Parent  1a3782e58489c66557234e9416ea99288b7c020d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 80eb79844e82da22ce44a2ee9c9f202bed0b94d1

diff -r 1a3782e58489 -r 41a49d4b2bc3 README.md
--- a/README.md	Wed Aug 11 09:23:24 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-GalaxyP - MaxQuant
-==================
-
-* Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
-* Tool ID: `maxquant`
-* Tool Type: `default`
-
-
-Description
------------
-
-Wrapper for the MaxQuant version available in conda.
-
-
-Updating
---------
-
-MaxQuant often changes the layout of its parameters file.
-So changes to the code are likely to be necessary when
-updating to a new version of MaxQuant. The init.py script
-can be used to initialize the tool with a new list of
-modifications or enzymes. From the tool dir run:
-
-./init.py -m MODIFICATIONS.XML -e ENZYMES.XML
-
-The location of these xml files usually is:
-ANACONDA_DIR/bin/conf/
\ No newline at end of file
diff -r 1a3782e58489 -r 41a49d4b2bc3 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Fri Jul 22 07:09:30 2022 +0000
@@ -0,0 +1,27 @@
+
+GalaxyP - MaxQuant
+==================
+
+
+* Home: https://github.com/galaxyproteomics/tools-galaxyp/
+* Tool ID: ``maxquant``
+* Tool Type: ``default``
+
+Description
+-----------
+
+Wrapper for the MaxQuant version available in conda.
+
+Updating
+--------
+
+MaxQuant often changes the layout of its parameters file.
+So changes to the code are likely to be necessary when
+updating to a new version of MaxQuant. The init.py script
+can be used to initialize the tool with a new list of
+modifications or enzymes. From the tool dir run:
+
+./init.py -m MODIFICATIONS.XML -e ENZYMES.XML
+
+The location of these xml files usually is:
+ANACONDA_DIR/bin/conf/
diff -r 1a3782e58489 -r 41a49d4b2bc3 macros.xml
--- a/macros.xml	Wed Aug 11 09:23:24 2021 +0000
+++ b/macros.xml	Fri Jul 22 07:09:30 2022 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0" ?>
 <macros>
     <token name="@VERSION@">1.6.17.0</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@VERSION_SUFFIX@">4</token>
     <token name="@VERSION_SUFFIX_MQPAR@">0</token>
     <token name="@VERSION_PTXQC@">1.0.10</token>
     <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
@@ -255,9 +255,6 @@
     </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="Phospho (STY)"/>
         <expand macro="mod_option" value="GlyGly (K)"/>
         <expand macro="mod_option" value="Methyl (KR)"/>
@@ -712,7 +709,6 @@
     </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="D.P"/>
@@ -878,4 +874,4 @@
             <citation type="doi">10.1021/acs.jproteome.5b00780</citation>
         </citations>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
diff -r 1a3782e58489 -r 41a49d4b2bc3 maxquant.xml
--- a/maxquant.xml	Wed Aug 11 09:23:24 2021 +0000
+++ b/maxquant.xml	Fri Jul 22 07:09:30 2022 +0000
@@ -384,6 +384,7 @@
                            help="Peptides containing only these modifications will be used for the quantification of proteins in addition to unmodified peptides. This includes ratio and intensity calculations including iBAQ">
                         <expand macro="default_mod_option" value="Oxidation (M)"/>
                         <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/>
+                        <expand macro="mod_option" value="Carbamidomethyl (C)"/>
                         <expand macro="modification"/>
                     </param>
                     <!-- note: the following default is different to the mquant default -->
@@ -431,7 +432,7 @@
 
 
         <repeat name="paramGroups" title="Parameter Group" min="1" default="1">
-            <param type="data" format="thermo.raw,mzXML,mzML" name="files" label="Infiles" multiple="true"
+            <param type="data" format="thermo.raw,mzxml,mzml" name="files" label="Infiles" multiple="true"
                    help="Only select infiles matching the filetype specified in the input options."/>
             <param type="integer" name="maxMissedCleavages"
                    label="missed cleavages" value="2"
@@ -439,14 +440,17 @@
             <param name="fixedModifications" type="select" label="fixed modifications"
                    multiple="true"
                    help="Select zero or more fixed modifications. They will always be attached to any occurence of the respective amino acid.">
+                <expand macro="mod_option" value="Acetyl (Protein N-term)"/>
+                <expand macro="default_mod_option" value="Carbamidomethyl (C)"/>
+                <expand macro="mod_option" value="Oxidation (M)"/>
                 <expand macro="modification"/>
-                <expand macro="default_mod_option" value="Carbamidomethyl (C)"/>
             </param>
             <param name="variableModifications" type="select" label="variable modifications"
                    multiple="true"
                    help="Select zero or more variable modifications. Do not specify label modifications here, neither ms1 level labels, like SILAC, nor isobaric labels.">
+                <expand macro="mod_option" value="Carbamidomethyl (C)"/>
                 <expand macro="default_mod_option" value="Oxidation (M)"/>
-                <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/>
+                <expand macro="mod_option" value="Acetyl (Protein N-term)"/>
                 <expand macro="modification"/>
             </param>
             <param name="enzymes" type="select" label="enzyme"
@@ -1008,9 +1012,9 @@
 
 **Input files**
 
-- Thermo raw, mzML, mzXMLfiles (in parameter group section)
+- Thermo raw, mzML, or mzXML files (in parameter group section)
 
-    - The datatype of all files has to be either 'thermo.raw', 'mzML' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
+    - The datatype of all files has to be either 'thermo.raw', 'mzml' or 'mzxml'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
 - Fasta file: specify parse rules according to your fasta file (header). Some examples for different fasta headers:  
 
                 ::