Mercurial > repos > galaxyp > peptideshaker
diff peptide_shaker.xml @ 54:7fdd9119cc4f draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e17bb5a0e4a22c7376b2e7a70cf690262a44a0c6"
| author | galaxyp |
|---|---|
| date | Thu, 20 Feb 2020 05:51:38 -0500 |
| parents | d67a3c1bfd09 |
| children | bb0130ff73ce |
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--- a/peptide_shaker.xml Wed May 08 14:06:07 2019 -0400 +++ b/peptide_shaker.xml Thu Feb 20 05:51:38 2020 -0500 @@ -30,7 +30,7 @@ peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI - --exec_dir="\$cwd/${bin_dir}" + --exec_dir="\$cwd/${bin_dir}" -temp_folder \$cwd/PathSettingsCLI -log \$cwd/peptideshaker.log && @@ -38,7 +38,7 @@ #set $output_reports_list = set(str($exporting_options.output_reports).split(',')) #else #set $output_reports_list = set() - #end if + #end if ###################### ## PeptideShakerCLI ## @@ -53,9 +53,9 @@ -identification_files \$cwd/searchgui_input.zip -id_params \$cwd/SEARCHGUI_IdentificationParameters.par -out \$cwd/peptideshaker_output.cpsx - #if $exporting_options.zip_conditional.zip_output_boolean == 'zip': - -zip \$cwd/peptideshaker_output.zip - #end if + #if $exporting_options.zip_conditional.zip_output_boolean == 'zip': + -zip \$cwd/peptideshaker_output.zip + #end if -threads "\${GALAXY_SLOTS:-12}" ##Optional processing parameters: @@ -135,7 +135,7 @@ && unzip \$cwd/peptideshaker_output.zip 'reports/*' -d \$cwd/output_reports #end if - #if len(output_reports_list)>0: + #if len($output_reports_list)>0: #if '0' in $output_reports_list: && find \$cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; #end if @@ -144,7 +144,7 @@ #end if #if '2' in $output_reports_list: && find \$cwd/output_reports -name '*Default_PSM_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \; - #end if` + #end if #if '3' in $output_reports_list: && find \$cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; #end if