Mercurial > repos > galaxyp > peptideshaker
diff peptide_shaker.xml @ 60:a6ff76e057fd draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62d0c9c13383dc58cc75cd273e0395e53a42b003"
| author | galaxyp |
|---|---|
| date | Tue, 20 Jul 2021 08:55:11 +0000 |
| parents | 943a34df6047 |
| children |
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--- a/peptide_shaker.xml Fri May 21 19:13:14 2021 +0000 +++ b/peptide_shaker.xml Tue Jul 20 08:55:11 2021 +0000 @@ -38,7 +38,9 @@ #if $optional_main_parameters.input_optional_identification_parameters: cp '${optional_main_parameters.input_optional_identification_parameters}' SEARCHGUI_IdentificationParameters.par && #else: - jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par && + ## Note that there will be just one .par file, the one (with unkown name) used thorought SG execution. We will rename it to a "standard" name + unzip -o searchgui_input.zip *.par && + mv *.par SEARCHGUI_IdentificationParameters.par && #end if ## Optional Fasta file #if $optional_main_parameters.input_fasta_file: @@ -68,7 +70,7 @@ ###################### ## PeptideShakerCLI ## ###################### - + ## TODO: --exec_dir may not be needed anymore. To be tested further (and maybe removed from the Conda package). peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI @@ -188,12 +190,12 @@ #end if #end if #end if - + ## Whilst non-blocking exception " /usr/local/share/peptide-shaker-2.0.25-0/resources/conf/paths.txt (Permission denied)" ## is fixed , we can avoid the process to be stopped by removing that message from the output - + | grep -v "resources/conf/paths.txt (Permission denied)" - + ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean): ## This unzipping command creates a reports folder into the current folder!