Mercurial > repos > galaxyp > meta_proteome_analyzer
changeset 3:763d5a3cd2b9 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer commit 271c77e5ec0b47c31d57b0d6f8e9b00cdbe11375"
| author | galaxyp |
|---|---|
| date | Tue, 07 Apr 2020 07:32:57 +0000 |
| parents | eeb17bb3d332 |
| children | c587a54c70ad |
| files | meta_proteome_analyzer.xml |
| diffstat | 1 files changed, 4 insertions(+), 11 deletions(-) [+] |
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--- a/meta_proteome_analyzer.xml Sat Mar 04 06:59:41 2017 -0500 +++ b/meta_proteome_analyzer.xml Tue Apr 07 07:32:57 2020 +0000 @@ -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>