# HG changeset patch
# User galaxyp
# Date 1586260146 14400
# Node ID 7fdfbf042ec6d9742df62e39c5871a836af10a36
# Parent  bea389f80d87bd039cab87c875af5e8021e9749b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer commit 271c77e5ec0b47c31d57b0d6f8e9b00cdbe11375"

diff -r bea389f80d87 -r 7fdfbf042ec6 meta_proteome_analyzer.xml
--- a/meta_proteome_analyzer.xml	Sat Mar 04 07:00:01 2017 -0500
+++ b/meta_proteome_analyzer.xml	Tue Apr 07 07:49:06 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="meta_proteome_analyzer" name="MetaProteomeAnalyzer" version="1.4.1">
+<tool id="meta_proteome_analyzer" name="MetaProteomeAnalyzer" version="1.4.1+galaxy1">
     <description>
         functional and taxonomic characterization of proteins
     </description>
@@ -7,8 +7,6 @@
     </requirements>
     <command>
 <![CDATA[
-        #set $temp_stderr = "mpa_stderr"
-
         cwd=`pwd` &&
         mkdir -p output_dir &&
         ## copy mpa conf dir to working dir
@@ -31,7 +29,7 @@
         ######################
         ## MPA ##
         ######################
-        (mpa-portable de.mpa.cli.CmdLineInterface -Djava.awt.headless=true -Xmx2048m
+        mpa-portable de.mpa.cli.CmdLineInterface -Djava.awt.headless=true -Xmx2048m
             -spectrum_files \$cwd
             -database input_database.fasta
             -missed_cleav $missed_cleavages
@@ -41,18 +39,13 @@
             -comet #if 'Comet' in $search_engines then 1 else 0#
             -msgf #if 'MSGF' in $search_engines then 1 else 0#
             -output_folder output_dir
-            -threads "\${GALAXY_SLOTS:-12}"
-         2> $temp_stderr) &&
+            -threads "\${GALAXY_SLOTS:-12}" &&
         mv ./output_dir/*_metaproteins.csv metaproteins.csv &&
         mv ./output_dir/*_metaprotein_taxa.csv metaprotein_taxa.csv &&
         mv ./output_dir/*_peptides.csv peptides.csv &&
         mv ./output_dir/*_proteins.csv proteins.csv &&
         mv ./output_dir/*_psms.csv psms.csv &&
-        mv ./output_dir/*_spectrum_ids.csv spectrum_ids.csv &&
-        exit_code_for_galaxy=\$? &&
-        cat $temp_stderr 2>&1 &&
-        (exit \$exit_code_for_galaxy)
-         
+        mv ./output_dir/*_spectrum_ids.csv spectrum_ids.csv
 ]]>
     </command>
     <inputs>