# HG changeset patch
# User galaxyp
# Date 1481841710 18000
# Node ID ecb9ec15083df91039a316123bf94220724fa0f5
# Parent  553f0336e43e54895b96ef05b1f2d8e46480db01
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999

diff -r 553f0336e43e -r ecb9ec15083d morpheus.xml
--- a/morpheus.xml	Mon May 23 09:51:47 2016 -0400
+++ b/morpheus.xml	Thu Dec 15 17:41:50 2016 -0500
@@ -41,8 +41,7 @@
     </macros>
 
     <requirements>
-        <requirement version="4.0">mono</requirement>
-        <requirement version="255">morpheus</requirement>
+        <requirement type="package" version="255">morpheus</requirement>
     </requirements>
 
     <stdio>
@@ -55,7 +54,7 @@
 
     <command><![CDATA[
         mkdir -p output_reports &&
-        cwd=`pwd`&&
+        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_mzml_mono_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":
             $advanced.noup
@@ -232,12 +234,12 @@
         <data name="output_protein_groups" format="tabular" label="${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"/>
@@ -246,14 +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"/>
@@ -270,7 +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"/>
@@ -287,7 +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"/>
diff -r 553f0336e43e -r ecb9ec15083d tool_dependencies.xml
--- a/tool_dependencies.xml	Mon May 23 09:51:47 2016 -0400
+++ /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="4912e4d532cd" name="package_mono_4_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="morpheus" version="255">
-       <repository changeset_revision="1beee9ed43fd" name="package_morpheus_255" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>