Mercurial > repos > galaxyp > peptideshaker
changeset 22:e3be595c0bf5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d
| author | iracooke |
|---|---|
| date | Fri, 07 Aug 2015 06:55:04 -0400 |
| parents | dfaea053e32f |
| children | 913dbf2b83e0 |
| files | peptide_shaker.xml searchgui.xml |
| diffstat | 2 files changed, 14 insertions(+), 6 deletions(-) [+] |
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--- a/peptide_shaker.xml Tue Jun 16 23:43:39 2015 -0400 +++ b/peptide_shaker.xml Fri Aug 07 06:55:04 2015 -0400 @@ -16,14 +16,18 @@ #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") #set $temp_stderr = "peptideshaker_stderr" + mkdir output_reports; cwd=`pwd`; + cp -r "\${PEPTIDESHAKER_JAR_PATH%/*}" bin; + tmp_peptideshaker_jar_path=`echo "\$cwd/bin/\${PEPTIDESHAKER_JAR_PATH\#\#/*/}"`; + ln -s '$searchgui_input' searchgui_input.zip && ###################### ## PeptideShakerCLI ## ###################### - (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI + (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.PeptideShakerCLI -temp_folder \$cwd/PeptideShakerCLI -experiment '$exp_str' -sample '$samp_str' @@ -80,7 +84,7 @@ #if 'mzidentML' in str($outputs).split(','): echo "Generating mzIdentML"; - (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI + (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.MzidCLI -in \$cwd/peptideshaker_output.zip -output_file output.mzid -contact_first_name "Proteomics" @@ -99,7 +103,7 @@ ## and will not be passed to the command line #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): - (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI + (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.ReportCLI -temp_folder \$cwd/ReportCLI -in \$cwd/peptideshaker_output.zip -out_reports \$cwd/output_reports
--- a/searchgui.xml Tue Jun 16 23:43:39 2015 -0400 +++ b/searchgui.xml Fri Aug 07 06:55:04 2015 -0400 @@ -20,6 +20,10 @@ mkdir output; mkdir output_reports; cwd=`pwd`; + + cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin; + tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`; + #for $mgf in $peak_lists: #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" ln -s -f '${mgf}' '${input_name}'; @@ -32,7 +36,7 @@ ########################################### #if $create_decoy: echo "Creating decoy database."; - java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && + java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta && ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; @@ -42,7 +46,7 @@ ## generate IdentificationParameters for SearchGUI ## ##################################################### - (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI + (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI -out SEARCHGUI_IdentificationParameters.parameters @GENERAL_PARAMETERS@ @@ -247,7 +251,7 @@ ################ ## Search CLI ## ################ - (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI + (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI -temp_folder `pwd` -spectrum_files \$cwd -output_folder \$cwd/output