# HG changeset patch
# User galaxyp
# Date 1481841698 18000
# Node ID f0202024f80b876717419adb70811f6e681a119b
# Parent  a7c58067f5eefea19ddd848a5bb50c27ec85febd
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999

diff -r a7c58067f5ee -r f0202024f80b morpheus.xml
--- a/morpheus.xml	Thu Nov 19 16:13:29 2015 -0500
+++ b/morpheus.xml	Thu Dec 15 17:41:38 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="morpheus" name="Morpheus" version="1.171.5">
+<tool id="morpheus" name="Morpheus" version="2.255.0">
     <description>database search algorithm for high-resolution tandem mass spectra</description>
     <macros>
         <xml name="modification_options">
@@ -41,8 +41,7 @@
     </macros>
 
     <requirements>
-        <requirement version="4.0">mono</requirement>
-        <requirement version="171">morpheus</requirement>
+        <requirement type="package" version="255">morpheus</requirement>
     </requirements>
 
     <stdio>
@@ -54,8 +53,8 @@
     </stdio>
 
     <command><![CDATA[
-        mkdir output_reports;
-        cwd=`pwd`;
+        mkdir -p output_reports &&
+        cwd=`pwd` &&
         #import re
         #set $searchdb_name = $searchdb
         #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension('uniprotxml').__class__): 
@@ -75,9 +74,12 @@
           && ln -s $input $input_name
         #end for
         #set $input_names = ','.join($input_list)
-        && mono \${MORPHEUS_PATH}/morpheus_cl.exe 
-        -d="$input_names"
-        -db=$searchdb_name
+        &&
+
+        mono `which morpheus`
+        -d='$input_names'
+        -db='$searchdb_name'
+
         #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension('uniprotxml').__class__): 
           #if str( $advanced.adv_options_selector) == "set":
             $advanced.noup
@@ -150,14 +152,16 @@
             -vm="$vmods"
         #end if
         -mt=\${GALAXY_SLOTS:-4}
-        #set $out_list = 'summary.tsv PSMs.tsv unique_peptides.tsv protein_groups.tsv log.txt *.pep.xml'
-        #if len($input_list) > 1:
-            && ( basepath=`grep 'Proteome Database:' log.txt  | sed 's/Proteome Database: \(.*\)${$searchdb_name}/\1/'`;
+        #set $out_list = 'log.txt summary.tsv aggregate.PSMs.tsv aggregate.unique_peptides.tsv aggregate.protein_groups.tsv aggregate.mzid *.pep.xml'
+        #if len($input_list) == 1:
+          && ln -s *.log.txt log.txt
+          && ln -s *.mzid aggregate.mzid 
+          && ln -s *.unique_peptides.tsv aggregate.unique_peptides.tsv
+          && ln -s *.protein_groups.tsv aggregate.protein_groups.tsv
+          && ln -s *.PSMs.tsv aggregate.PSMs.tsv
+        #end if
+          && ( basepath=`grep 'Proteome Database:' log.txt  | sed 's/Proteome Database: \(.*\)${$searchdb_name}/\1/'`;
              for i in $out_list; do cat \$i | sed "s#\${basepath}\##" > output_reports/\$i; done )
-        #else 
-            && ( basepath=`grep 'Proteome Database:' *.log.txt  | head -1 | sed 's/Proteome Database: \(.*\)${$searchdb_name}/\1/'`;
-             for i in $out_list; do cat *\$i | sed "s#\${basepath}\##" > output_reports/\$i; done )
-        #end if
     ]]></command>
     <inputs>
         <param name="inputs" type="data" format="mzml" multiple="true" label='Indexed mzML' />
@@ -223,18 +227,19 @@
         </conditional>
     </inputs>
     <outputs>
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: log.txt" from_work_dir="output_reports/log.txt" />
         <data name="summary" format="txt" label="${tool.name} on ${on_string}: summary.tsv" from_work_dir="output_reports/summary.tsv" />
-        <data name="log" format="txt" label="${tool.name} on ${on_string}: log.txt" from_work_dir="output_reports/log.txt" />
-        <data name="output_psms" format="tabular" label="${tool.name} on ${on_string}: PSMs.tsv" from_work_dir="output_reports/PSMs.tsv" />
-        <data name="output_unique_peptides" format="tabular" label="${tool.name} on ${on_string}: unique_peptides.tsv" from_work_dir="output_reports/unique_peptides.tsv" />
-        <data name="output_protein_groups" format="tabular" label="${tool.name} on ${on_string}: protein_groups.tsv" from_work_dir="output_reports/protein_groups.tsv" />
+        <data name="output_psms" format="tabular" label="${tool.name} on ${on_string}: PSMs.tsv" from_work_dir="output_reports/aggregate.PSMs.tsv" />
+        <data name="output_unique_peptides" format="tabular" label="${tool.name} on ${on_string}: unique_peptides.tsv" from_work_dir="output_reports/aggregate.unique_peptides.tsv" />
+        <data name="output_protein_groups" format="tabular" label="${tool.name} on ${on_string}: protein_groups.tsv" from_work_dir="output_reports/aggregate.protein_groups.tsv" />
+        <data name="aggregate_mzid" format="mzid" label="${tool.name} on ${on_string}: aggregate.mzid" from_work_dir="output_reports/aggregate.mzid" />
         <collection name="morpheus_pep_xmls" type="list" label="${tool.name} on ${on_string} pep.xml">
-            <discover_datasets pattern="(?P&lt;name&gt;.*\.pep.xml)" ext="pepxml" visible="False" directory="output_reports" />
+            <discover_datasets pattern="(?P&lt;name&gt;.*\.pep.xml)" ext="pepxml" visible="false" directory="output_reports" />
         </collection>
     </outputs>
     <tests>
         <test>
-            <param name="input" value="test_input.mzML" ftype="mzml"/>
+            <param name="inputs" value="test_input.mzML" ftype="mzml"/>
             <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
             <param name="fdr" value="1"/>
             <param name="mvmi" value="1024"/>
@@ -243,14 +248,14 @@
             <param name="precmtv" value="2.5"/>
             <output name="output_psms">
                 <assert_contents>
-                    <has_text text="K.TTGSSSSSSSK.K" />
-                    <not_has_text text="carbamidomethylation of C" />
-                    <not_has_text text="(oxidation of M)" />
+                    <not_has_text text="K.TTGSSSSSSSK.K" />
+                    <has_text text="carbamidomethylation of C" />
+                    <has_text text="(oxidation of M)" />
                 </assert_contents>
             </output>
         </test>
         <test>
-            <param name="input" value="test_input.mzML" ftype="mzml"/>
+            <param name="inputs" value="test_input.mzML" ftype="mzml"/>
             <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
             <param name="fdr" value="1"/>
             <param name="mvmi" value="1024"/>
@@ -267,7 +272,7 @@
             </output>
         </test>
         <test>
-            <param name="input" value="test_input.mzML" ftype="mzml"/>
+            <param name="inputs" value="test_input.mzML" ftype="mzml"/>
             <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
             <param name="fdr" value="1"/>
             <param name="mvmi" value="1024"/>
@@ -284,7 +289,7 @@
             </output>
         </test>
         <test>
-            <param name="input" value="test_input.mzML" ftype="mzml"/>
+            <param name="inputs" value="test_input.mzML" ftype="mzml"/>
             <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
             <param name="fdr" value="1"/>
             <param name="mvmi" value="1024"/>
@@ -297,8 +302,8 @@
             <param name="prodmtv" value=".01"/>
             <output name="output_psms">
                 <assert_contents>
-                    <has_text text="K.KYFLENKIGTDR.R" />
-                    <not_has_text text="R.KRSLFDS(UniProt: Phosphoserine)AFSSR.A" />
+                    <has_text text="K.KTLKSDGVAGLYR.G" />
+                    <not_has_text text="K.RSPSGNISTNSMR.P" />
                 </assert_contents>
             </output>
         </test>
diff -r a7c58067f5ee -r f0202024f80b tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 19 16:13:29 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="mono" version="4.0">
-       <repository changeset_revision="d081ac7d12d1" name="package_mono_4_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="morpheus" version="171">
-       <repository changeset_revision="a8e9d3b708f2" name="package_morpheus_171" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>