diff macros.xml @ 21:8934bc76bb52 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb

--- a/macros.xml	Tue Jan 31 18:14:40 2023 +0000
+++ b/macros.xml	Mon Jun 19 17:02:17 2023 +0000
@@ -1,9 +1,10 @@
 <?xml version="1.0" ?>
 <macros>
-    <token name="@VERSION@">1.6.17.0</token>
-    <token name="@VERSION_SUFFIX@">7</token>
-    <token name="@VERSION_SUFFIX_MQPAR@">2</token>
-    <token name="@VERSION_PTXQC@">1.0.10</token>
+    <token name="@PROFILE@">21.05</token>
+    <token name="@VERSION@">2.0.3.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX_MQPAR@">0</token>
+    <token name="@VERSION_PTXQC@">1.0.16</token>
     <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
     <token name="@TMT2PLEX@">
                     - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
@@ -90,8 +91,8 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">maxquant</requirement>
-            <requirement type="package" version="3.7">python</requirement>
-            <requirement type="package" version="5.1.2">pyyaml</requirement>
+            <requirement type="package" version="5.4.1">pyyaml</requirement>
+            <requirement type="package" version="3.1.418">dotnet</requirement>
             <requirement type="package" version="@VERSION_PTXQC@">r-ptxqc</requirement>
             <requirement type="package" version="1.32">tar</requirement>
         </requirements>
@@ -116,25 +117,25 @@
                 AddPageNumbers: 'on'
             File:
               Parameters:
-              #if $qc.do_it:
+              #if $qc.do_it == "true":
                 enabled: ${qc.parameters}
               #end if
               Summary:
-              #if $qc.do_it:
+              #if $qc.do_it == "true":
                 enabled: ${qc.summary}
               #end if
                 IDRate:
                   Thresh_bad_num: 20.0
                   Thresh_great_num: 35.0
               ProteinGroups:
-              #if $qc.do_it:
+              #if $qc.do_it == "true":
                 enabled: ${qc.proteingroups}
               #end if
                 RatioPlot:
                   LabelIncThresh_num: 4.0
                 IntensityThreshLog2_num: 25.0
               Evidence:
-              #if $qc.do_it:
+              #if $qc.do_it == "true":
                 enabled: ${qc.evidence}
               #end if
                 ProteinCountThresh_num: 3500.0
@@ -161,11 +162,11 @@
                 firstSearch_outOfCalWarnSD_num: 2.0
                 MQpar_mainSearchTol_num: 4.5
               MsMs:
-              #if $qc.do_it:
+              #if $qc.do_it == "true":
                 enabled: ${qc.msms}
               #end if
               MsMsScans:
-              #if $qc.do_it:
+              #if $qc.do_it == "true":
                 enabled: ${qc.msmsscans}
               #end if
                 IonInjectionThresh_num: 10.0
@@ -222,7 +223,10 @@
     </xml>
     <xml name="ptxqc-opts">
         <conditional name="qc">
-            <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" type="boolean" checked="false"/>
+            <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" type="select">
+                <option value="true">True</option>
+                <option value="false" selected="true">False</option>
+            </param>
             <when value="true">
                 <param name="parameters" type="boolean" checked="true" label="use parameters.txt?" truevalue="yes" falsevalue="no"/>
                 <param name="summary" type="boolean" checked="true" label="use summary.txt?" truevalue="yes" falsevalue="no"/>
@@ -234,6 +238,18 @@
             <when value="false"/>
         </conditional>
     </xml>
+
+    <xml name="output" tokens="name,label" token_format="tabular">
+        <data format="@FORMAT@" label="${on_string}: @LABEL@" name="@NAME@">
+            <filter>'@NAME@' in output_opts['output']</filter>
+        </data>
+    </xml>
+    <xml name="output_from_wdir" tokens="name,label" token_ext="txt" token_format="tabular">
+        <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="${on_string}: @LABEL@" name="@NAME@">
+            <filter>'@NAME@' in output_opts['output']</filter>
+        </data>
+    </xml>
+
     <xml name="outputs">
         <outputs>
             <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/>
@@ -242,7 +258,7 @@
             <expand macro="output_from_wdir" name="evidence" label="MaxQuant Evidence"/>
             <expand macro="output_from_wdir" name="parameters" label="MaxQuant Tabular Parameters"/>
             <expand macro="output_from_wdir" name="msms" label="MaxQuant MSMS"/>
-            <expand macro="output_from_wdir" name="mzTab" label="mzTab" ext="mzTab"/>
+            <expand macro="output_from_wdir" name="mzTab" label="mzTab" format="mztab" ext="mzTab"/>
             <expand macro="output_from_wdir" name="allPeptides" label="all peptides"/>
             <expand macro="output_from_wdir" name="libraryMatch" label="library match"/>
             <expand macro="output_from_wdir" name="matchedFeatures" label="matched features"/>
@@ -256,7 +272,7 @@
             <expand macro="output" name="log" format="txt" label="log"/>
             <expand macro="output" name="config" format="txt" label="yaml config file"/>
             <data format="pdf" label="PTXQC report for ${on_string}" name="ptxqc_report">
-                <filter>qc['do_it'] == True</filter>
+                <filter>qc['do_it'] == "true"</filter>
             </data>
         </outputs>
     </xml>
@@ -853,6 +869,67 @@
         <expand macro="mod_option" value="TMTpro18plex-Lys134C"/>
         <expand macro="mod_option" value="TMTpro18plex-Lys135N"/>
     </xml>
+
+    <xml name="reporter_ion_macro">
+        <conditional name="iso_labels">
+            <param name="labeling" type="select" label="isobaric labeling"
+                   help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">
+                <option value="custom">custom</option>
+                <option value="tmt2plex">TMT2plex</option>
+                <option value="tmt6plex">TMT6plex</option>
+                <option value="tmt8plex">TMT8plex</option>
+                <option value="tmt10plex">TMT10plex</option>
+                <option value="tmt11plex">TMT11plex</option>
+                <option value="tmtpro16plex">TMTpro16plex</option>
+                <option value="tmtpro18plex">TMTpro18plex</option>
+                <option value="itraq4plex">iTRAQ4plex</option>
+                <option value="itraq8plex">iTRAQ8plex</option>
+                <option value="iodotmt6plex">iodoTMT6plex</option>
+            </param>
+            <when value="tmt2plex"/>
+            <when value="tmt6plex"/>
+            <when value="tmt8plex"/>
+            <when value="tmt10plex"/>
+            <when value="tmt11plex"/>
+            <when value="tmtpro16plex"/>
+            <when value="tmtpro18plex"/>
+            <when value="itraq4plex"/>
+            <when value="itraq8plex"/>
+            <when value="iodotmt6plex"/>
+            <when value="custom">
+                <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
+                    <param name="internallabel" type="select" label="internal label" help="contains Lys">
+                        <expand macro="iso_labels"/>
+                    </param>
+                    <param name="terminallabel" type="select" label="terminal label" help="contains Nter">
+                        <option value="">None</option>
+                        <expand macro="iso_labels"/>
+                    </param>
+                    <param name="cm2" type="float" label="correction factor -2%" value="0.0"/>
+                    <param name="cm1" type="float" label="correction factor -1%" value="0.0"/>
+                    <param name="cp1" type="float" label="correction factor +1%" value="0.0"/>
+                    <param name="cp2" type="float" label="correction factor +2%" value="0.0"/>
+                    <param type="boolean" name="tmtlike" checked="false"
+                           label="TMT-like"
+                           truevalue="True" falsevalue="False"/>
+                </repeat>
+            </when>
+        </conditional>
+        <conditional name="filter_by_pif">
+            <param name="filter_pif" type="select" label="Filter by PIF"
+                    help="If checked, quantified PSMs will be filtered by their precursor intensity fraction to avoid using peptides that clearly suffer from co-fragmentation with other peptide species.">
+                    <option value="True">True</option>
+                    <option value="False" selected="true">False</option>
+            </param>
+            <when value="True">
+                <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0"
+                       max="1"
+                       help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
+            </when>
+            <when value="False"/>
+        </conditional>
+    </xml>
+
     <xml name="citations">
         <citations>
             <citation type="bibtex">