# HG changeset patch
# User galaxyp
# Date 1586215114 14400
# Node ID 622dd6d510328e126107df7a2471962abbfbf08f
# Parent  a2ab72e994dc62916e3a23cac8cfac4269b2a3aa
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967"

diff -r a2ab72e994dc -r 622dd6d51032 pathwaymatcher.xml
--- a/pathwaymatcher.xml	Sun Aug 04 15:52:53 2019 -0400
+++ b/pathwaymatcher.xml	Mon Apr 06 19:18:34 2020 -0400
@@ -4,7 +4,7 @@
     </description>
     <macros>
        <token name="@PATHWAYMATCHER_VERSION@">1.9.1</token>
-       <token name="@TOOL_SUBVERSION@">3</token>
+       <token name="@TOOL_SUBVERSION@">4</token>
        <xml name="input_fasta">
          <param format="fasta" name="input_database" type="data" label="Protein Database"
              help="Select FASTA database from history"/>
@@ -13,6 +13,7 @@
     <requirements>
         <requirement type="package" version="@PATHWAYMATCHER_VERSION@">pathwaymatcher</requirement>
         <requirement type="package" version="3.0">zip</requirement>
+        <requirement type="package" version="8.31">coreutils</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Job Failed" />
@@ -37,18 +38,17 @@
         ## If we use peptideshaker 2.x files as inputs, firstly we need to uncompress their proteoforms files.
         #for $i, $s in enumerate($match_types)
             #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms"
-                unzip -j '${$s.match_type.input_peptideshakerzip_proteoforms}' 'reports/proteins_proteoforms.txt' -d './';
-                mv proteins_proteoforms.txt ps_proteoforms_'${$i}'.txt;
+                unzip -j '${$s.match_type.input_peptideshakerzip_proteoforms}' 'reports/proteins_proteoforms.txt' -d './' &&
+                mv proteins_proteoforms.txt ps_proteoforms_'${$i}'.txt &&
             #end if
         #end for
 
         #####################
         ## Pathway Matcher ##
         #####################
-        (pathwaymatcher
+        pathwaymatcher
 
             #for $i, $s in enumerate($match_types)
-
                 ## PROTEOFORMS
 
                 #if $s.match_type.match_type_selector == "proteoforms"
@@ -116,8 +116,6 @@
                     -m '${s.match_type.modifiedpeptide_match_criteria}'
                     -r '${s.match_type.modifiedpeptide_ptm_range}'
                 #end if
-
-
             #end for
 
             ## OUTPUT OPTIONS
@@ -140,29 +138,22 @@
                 -gp
             #end if
 
-        2>> $temp_stderr);
-
         ## We create a folder to contain graphs files.
         #if $output_options.output_graphs:
-            mkdir "graphs";
+            && mkdir "graphs"
         #end if
         #if 'gg' in $output_graphs_list:
-            mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv" ;
+            && mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv"
         #end if
         #if 'gu' in $output_graphs_list:
-            mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv";
+            && mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv"
         #end if
         #if 'gp' in $output_graphs_list:
-            mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv";
+            && mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv"
         #end if
-
-        exit_code_for_galaxy=\$?;
-        cat $temp_stderr 2>&1;
-        (exit \$exit_code_for_galaxy)
 ]]>
     </command>
     <inputs>
-
         <repeat name="match_types" title="Match" min="1">
             <conditional name="match_type">
                   <param name="match_type_selector" type="select" label="Match type"
@@ -179,7 +170,6 @@
                       <option value="modifiedpeptide">Peptides - Peptide List with PTM types and sites</option>
                   </param>
 
-
                   <!-- Proteoforms  -->
                   <when value="proteoforms">
                       <param format="txt" name="input_proteoforms" type="data" label="Proteoforms"