1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b99d93d0f137/ changeset: b99d93d0f137 user: jgoecks date: 2013-01-25 00:02:22 summary: Cuffcompare wrapper fixes + update test files for v2.0.2 affected #: 2 files
diff -r 5fda62776e3d09702d18ba7a1e4a106425949f15 -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec test-data/cuffcompare_out7.txt --- a/test-data/cuffcompare_out7.txt +++ b/test-data/cuffcompare_out7.txt @@ -1,5 +1,5 @@ -# Cuffcompare v1.3.0 | Command line was: -#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/010/dataset_10703.dat -R ./input1 ./input2 +# Cuffcompare v2.0.2 | Command line was: +#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/002/dataset_2770.dat -R ./input1 ./input2 #
#= Summary for dataset: ./input1 :
diff -r 5fda62776e3d09702d18ba7a1e4a106425949f15 -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -78,7 +78,7 @@ <outputs><data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" from_work_dir="cc_output.stats" /> - <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: ${first_input.hid} data tmap file" + <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: data ${first_input.hid} tmap file" from_work_dir="cc_output.input1.tmap" /><data format="tabular" name="input1_refmap" label="${tool.name} on ${on_string}: data ${first_input.hid} refmap file" @@ -86,12 +86,12 @@ <filter>annotation['use_ref_annotation'] == 'Yes'</filter></data><data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} tmap file" from_work_dir="cc_output.input2.tmap"> - <filter>len( input_files ) > 1</filter> + <filter>len( input_files ) >= 1</filter></data><data format="tabular" name="input2_refmap" label="${tool.name} on ${on_string}: data ${input_files[0]['additional_input'].hid} refmap file" from_work_dir="cc_output.input2.refmap"> - <filter>annotation['use_ref_annotation'] == 'Yes' and len( input_files ) > 1</filter> + <filter>annotation['use_ref_annotation'] == 'Yes' and len( input_files ) >= 1</filter></data><data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking"><filter>len( input_files ) > 0</filter>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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