2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/46fc972bb869/ changeset: 46fc972bb869 user: jgoecks date: 2013-01-14 19:56:50 summary: Improve error message for test parameters that could not be added. affected #: 1 file diff -r f57b2bfb2365bef93b7974d990d663a0660a67d9 -r 46fc972bb869a4d3807bc11dcad7f279efc3a878 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -35,11 +35,13 @@ value = new_value break if not found_parameter: - raise ValueError( "Unable to determine parameter type of test input '%s'. Ensure that the parameter exists and that any container groups are defined first." % name ) + raise ValueError( "Unable to determine parameter type of test input '%s'. " + "Ensure that the parameter exists and that any container groups are defined first." + % name ) elif isinstance( self.tool.inputs[name], basic.DataToolParameter ): value = self.__add_uploaded_dataset( name, value, extra, self.tool.inputs[name] ) except Exception, e: - log.debug( "Error in add_param for %s: %s" % ( name, e ) ) + log.debug( "Error for tool %s: could not add test parameter %s. %s" % ( self.tool.id, name, e ) ) self.inputs.append( ( name, value, extra ) ) def add_output( self, name, file, extra ): self.outputs.append( ( name, file, extra ) ) https://bitbucket.org/galaxy/galaxy-central/commits/58e3f00d02b8/ changeset: 58e3f00d02b8 user: jgoecks date: 2013-01-14 19:57:19 summary: Fix issues in Tophat color wrapper tests. affected #: 1 file diff -r 46fc972bb869a4d3807bc11dcad7f279efc3a878 -r 58e3f00d02b8c09da2f1172fcadb7c8e65493ee3 tools/ngs_rna/tophat_color_wrapper.xml --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -503,7 +503,7 @@ <!-- Test color-space single-end reads with pre-built index and full parameters --><test><!-- Tophat commands: - tophat -p 1 -C -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +allow-indels +coverage-search +min-coverage-intron 50 +max-coverage-intron 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search partialMm9chrX_random_cs test-data/tophat_in4.fastqcssanger + tophat -p 1 -C -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +allow-indels +coverage-search +min-coverage-intron 50 +max-coverage-intron 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intron 5000 +microexon-search partialMm9chrX_random_cs test-data/tophat_in4.fastqcssanger Replace the + with double-dash Rename the files in tmp_dir appropriately --> @@ -564,7 +564,7 @@ <!-- TopHat commands: cp test-data/tophat_in5.fasta tophat_in5.fa bowtie-build -C -f tophat_in5.fa tophat_in5 - tophat -C -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +library-type fr-unstranded +allow-indels +coverage-search +min-coverage-intron 50 +max-coverage-intron 15000 +mate-std-dev 20 +segment-mismatch 2 +segment-length 20 +min-segment-intron 50 +max-segment-intron 500000 tophat_in5 test-data/tophat_in6.fastqcssanger test-data/tophat_in7.fastqcssanger + tophat -C -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +library-type fr-unstranded +allow-indels +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intron 5000 +coverage-search +min-coverage-intron 50 +max-coverage-intron 15000 +mate-std-dev 20 +segment-mismatch 2 +segment-length 20 +min-segment-intron 50 +max-segment-intron 500000 tophat_in5 test-data/tophat_in6.fastqcssanger test-data/tophat_in7.fastqcssanger Replace the + with double-dash Rename the files in tmp_dir appropriately --> @@ -591,7 +591,10 @@ <param name="max_insertion_length" value="3"/><param name="max_deletion_length" value="3"/><param name="use_junctions" value="No" /> - <param name="use_search" value="No" /> + <param name="use_search" value="Yes" /> + <param name="min_closure_exon" value="50" /> + <param name="min_closure_intron" value="50" /> + <param name="max_closure_intron" value="5000" /><param name="use_search" value="Yes" /><param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /> 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.