details: http://www.bx.psu.edu/hg/galaxy/rev/7151ae06bf7a changeset: 3692:7151ae06bf7a user: jeremy goecks <jeremy.goecks@emory.edu> date: Sat Apr 24 15:03:22 2010 -0400 description: Better labels for rna-seq tools' output datasets. diffstat: tools/ngs_rna/cuffcompare_wrapper.py | 4 +++- tools/ngs_rna/cuffcompare_wrapper.xml | 6 +++--- tools/ngs_rna/cuffdiff_wrapper.py | 4 +++- tools/ngs_rna/cuffdiff_wrapper.xml | 22 +++++++++++----------- tools/ngs_rna/cufflinks_wrapper.py | 4 +++- tools/ngs_rna/cufflinks_wrapper.xml | 6 +++--- tools/ngs_rna/tophat_wrapper.xml | 6 +++--- 7 files changed, 29 insertions(+), 23 deletions(-) diffs (130 lines): diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.py Sat Apr 24 15:03:22 2010 -0400 @@ -33,11 +33,13 @@ if options.ignore_nonoverlap: cmd += " -R " + # Output/debugging. + print cmd + # Add input files. if type(args) is list: args = " ".join(args) cmd += " " + args - print cmd # Run command. try: diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Sat Apr 24 15:03:22 2010 -0400 @@ -32,9 +32,9 @@ </inputs> <outputs> - <data format="gtf" name="transcripts_combined" label="Cuffcompare on data ${input1.hid} and data ${input2.hid}: combined transcripts"/> - <data format="tracking" name="transcripts_tracking" label="Cuffcompare on data ${input1.hid} and data ${input2.hid}: transcript tracking"/> - <data format="gtf" name="transcripts_accuracy" label="Cuffcompare on data ${input1.hid} and data ${input2.hid}: transcript accuracy"/> + <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/> + <data format="tracking" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking"/> + <data format="gtf" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy"/> </outputs> <tests> diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.py Sat Apr 24 15:03:22 2010 -0400 @@ -69,9 +69,11 @@ if options.max_mle_iterations: cmd += ( " --max-mle-iterations %i" % int ( options.max_mle_iterations ) ) + # Output/debugging. + print cmd + # Add inputs. cmd += " " + options.inputA + " " + options.input1 + " " + options.input2 - print cmd # Run command. try: diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Sat Apr 24 15:03:22 2010 -0400 @@ -44,17 +44,17 @@ </inputs> <outputs> - <data format="tabular" name="isoforms_exp" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: isoform expression"/> - <data format="tabular" name="genes_exp" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: gene expression"/> - <data format="tabular" name="tss_groups_exp" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: TSS groups expression"/> - <data format="tabular" name="cds_exp_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: CDS Expression FPKM Tracking"/> - <data format="tabular" name="splicing_diff" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: splicing diff"/> - <data format="tabular" name="cds_diff" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: CDS diff"/> - <data format="tabular" name="promoters_diff" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: promoters diff"/> - <data format="tabular" name="tss_groups_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: TSS groups FPKM tracking" /> - <data format="tabular" name="cds_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: CDS FPKM tracking"/> - <data format="tabular" name="genes_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: gene FPKM tracking"/> - <data format="tabular" name="isoforms_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: isoform FPKM tracking"/> + <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: isoform expression"/> + <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene expression"/> + <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups expression"/> + <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS Expression FPKM Tracking"/> + <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing diff"/> + <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS diff"/> + <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters diff"/> + <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" /> + <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking"/> + <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking"/> + <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: isoform FPKM tracking"/> </outputs> <tests> diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cufflinks_wrapper.py --- a/tools/ngs_rna/cufflinks_wrapper.py Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.py Sat Apr 24 15:03:22 2010 -0400 @@ -62,9 +62,11 @@ if options.max_mle_iterations: cmd += ( " --max-mle-iterations %i" % int ( options.max_mle_iterations ) ) + # Output/debugging. + print cmd + # Add input files. cmd += " " + options.input - print cmd # Run command. try: diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Sat Apr 24 15:03:22 2010 -0400 @@ -50,9 +50,9 @@ </inputs> <outputs> - <data format="expr" name="genes_expression" label="Cufflinks on data ${input.hid}: gene expression"/> - <data format="expr" name="transcripts_expression" label="Cufflinks on data ${input.hid}: transcript expression"/> - <data format="gtf" name="assembled_isoforms" label="Cufflinks on data ${input.hid}: assembled transcripts"/> + <data format="expr" name="genes_expression" label="${tool.name} on ${on_string}: gene expression"/> + <data format="expr" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression"/> + <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/> </outputs> <tests> diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/tophat_wrapper.xml Sat Apr 24 15:03:22 2010 -0400 @@ -55,9 +55,9 @@ </inputs> <outputs> - <data format="sam" name="accepted_hits"/> - <data format="wig" name="coverage" /> - <data format="bed" name="junctions" /> + <data format="sam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> + <data format="wig" name="coverage" label="${tool.name} on ${on_string}: coverage"/> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/> </outputs> <tests>