1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/be48d8761458/ changeset: be48d8761458 user: jgoecks date: 2011-06-22 14:36:48 summary: Better handling of Cuffdiff outputs when set_metadata_externally=True affected #: 2 files (297 bytes) --- a/tools/ngs_rna/cuffcompare_wrapper.py Tue Jun 21 16:22:14 2011 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.py Wed Jun 22 08:36:48 2011 -0400 @@ -32,6 +32,9 @@ parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) + # Outputs. + parser.add_option( '', '--combined-transcripts', dest='combined_transcripts' ) + (options, args) = parser.parse_args() # output version # of tool @@ -115,6 +118,9 @@ if returncode != 0: raise Exception, stderr + # Copy outputs. + shutil.copyfile( "cc_output.combined.gtf" , options.combined_transcripts ) + # check that there are results in the output file cc_output_fname = "cc_output.stats" if len( open( cc_output_fname, 'rb' ).read().strip() ) == 0: --- a/tools/ngs_rna/cuffcompare_wrapper.xml Tue Jun 21 16:22:14 2011 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Wed Jun 22 08:36:48 2011 -0400 @@ -26,11 +26,15 @@ --index_dir=${GALAXY_DATA_INDEX_DIR} #end if + ## Outputs. + --combined-transcripts=${transcripts_combined} + ## Inputs. ${first_input} #for $input_file in $input_files: ${input_file.additional_input} #end for + </command><inputs><param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/> @@ -86,7 +90,7 @@ <data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking"><filter>len( input_files ) > 0</filter></data> - <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts" from_work_dir="cc_output.combined.gtf"/> + <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/></outputs><tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.