diff maxquant.xml @ 16:74f5d355d156 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 80eb79844e82da22ce44a2ee9c9f202bed0b94d1

--- a/maxquant.xml	Wed Aug 11 09:24:23 2021 +0000
+++ b/maxquant.xml	Fri Jul 22 07:10:28 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:  
 
                 ::