# HG changeset patch
# User galaxyp
# Date 1488628781 18000
# Node ID eeb17bb3d3326143b54f36d0945eb461ae5e837a
# Parent  b41e6d379c5f367b9edb24f80fb797571626eb25
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer commit 69cfb20d049ddeccef197865cc07eac5363ea8ea

diff -r b41e6d379c5f -r eeb17bb3d332 meta_proteome_analyzer.xml
--- a/meta_proteome_analyzer.xml	Fri Mar 03 14:57:59 2017 -0500
+++ b/meta_proteome_analyzer.xml	Sat Mar 04 06:59:41 2017 -0500
@@ -9,25 +9,24 @@
 <![CDATA[
         #set $temp_stderr = "mpa_stderr"
 
-        cwd=`pwd`;
-        mkdir -p output_dir;
+        cwd=`pwd` &&
+        mkdir -p output_dir &&
         ## copy mpa conf dir to working dir
-        jar_dir=`mpa-portable -get_jar_dir`;
-        cp -R \$jar_dir/conf .;
+        jar_dir=`mpa-portable -get_jar_dir` &&
+        cp -R \$jar_dir/conf . &&
 
         ## echo the search engines to run
         #set $search_engines = str($search_engines_options.engines).split(',')
-        echo "$search_engines_options.engines";
-        echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";
+        echo "$search_engines_options.engines" &&
+        echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}" &&
 
         #for $mgf in $peak_lists:
             #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
-            ln -s -f '${mgf}' '${input_name}';
+            ln -s -f '${mgf}' '${input_name}' &&
             #set $encoded_id = $__app__.security.encode_id($mgf.id)
-            echo "Spectrums:${mgf.display_name}(API:${encoded_id}) ";
+            echo "Spectrums:${mgf.display_name}(API:${encoded_id}) " &&
         #end for
-        ##ln -s "${input_database}" input_database.fasta;
-        cp "${input_database}" input_database.fasta;
+        cp "${input_database}" input_database.fasta &&
 
         ######################
         ## MPA ##
@@ -44,14 +43,14 @@
             -output_folder output_dir
             -threads "\${GALAXY_SLOTS:-12}"
          2> $temp_stderr) &&
-        find \$cwd/output_dir -name '*_metaproteins.csv' -exec bash -c 'mv "$0" "metaproteins.csv"' {} \; ;
-        find \$cwd/output_dir -name '*_metaprotein_taxa.csv' -exec bash -c 'mv "$0" "metaprotein_taxa.csv"' {} \; ;
-        find \$cwd/output_dir -name '*_peptides.csv' -exec bash -c 'mv "$0" "peptides.csv"' {} \; ;
-        find \$cwd/output_dir -name '*_proteins.csv' -exec bash -c 'mv "$0" "proteins.csv"' {} \; ;
-        find \$cwd/output_dir -name '*_psms.csv' -exec bash -c 'mv "$0" "psms.csv"' {} \; ;
-        find \$cwd/output_dir -name '*_spectrum_ids.csv' -exec bash -c 'mv "$0" "spectrum_ids.csv"' {} \; ;
-        exit_code_for_galaxy=\$?;
-        cat $temp_stderr 2>&1;
+        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)
          
 ]]>
@@ -170,7 +169,7 @@
 * proteins
 * spectrum_ids
 * metaproteins
-*metaprotein_taxa
+* metaprotein_taxa
 
 
 ------
diff -r b41e6d379c5f -r eeb17bb3d332 test-data/._Test416Ebendorf.mgf
Binary file test-data/._Test416Ebendorf.mgf has changed