Mercurial > repos > galaxyp > meta_proteome_analyzer
changeset 2:eeb17bb3d332 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer commit 69cfb20d049ddeccef197865cc07eac5363ea8ea
| author | galaxyp |
|---|---|
| date | Sat, 04 Mar 2017 06:59:41 -0500 |
| parents | b41e6d379c5f |
| children | 763d5a3cd2b9 |
| files | meta_proteome_analyzer.xml test-data/._Test416Ebendorf.mgf |
| diffstat | 2 files changed, 18 insertions(+), 19 deletions(-) [+] |
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--- 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 ------