Mercurial > repos > galaxyp > peptideshaker
diff peptide_shaker.xml @ 12:d298e0b6fd72 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
| author | iracooke |
|---|---|
| date | Tue, 11 Aug 2015 15:55:30 -0400 |
| parents | 9d12b1d3c4ef |
| children | 3ccfbb673089 |
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--- a/peptide_shaker.xml Tue Jun 16 23:43:15 2015 -0400 +++ b/peptide_shaker.xml Tue Aug 11 15:55:30 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