1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/8ecfa22f0d98/ changeset: r5075:8ecfa22f0d98 user: jgoecks date: 2011-02-17 03:46:23 summary: Fix bug in extract_genomic_dna to handle non-GFF files when interpret features is true. Tweak functional test to cover new behavior. affected #: 2 files (16 bytes)
--- a/tools/extract/extract_genomic_dna.py Wed Feb 16 13:50:30 2011 -0500 +++ b/tools/extract/extract_genomic_dna.py Wed Feb 16 21:46:23 2011 -0500 @@ -234,7 +234,7 @@ fout.write( "%s\n" % str( sequence[c:b] ) ) c = b else: # output_format == "interval" - if interpret_features: + if gff_format and interpret_features: # TODO: need better GFF Reader to capture all information needed # to produce this line. meta_data = "\t".join(
--- a/tools/extract/extract_genomic_dna.xml Wed Feb 16 13:50:30 2011 -0500 +++ b/tools/extract/extract_genomic_dna.xml Wed Feb 16 21:46:23 2011 -0500 @@ -70,7 +70,7 @@ </test><test><param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> - <param name="interpret_features" value="no"/> + <param name="interpret_features" value="yes"/><param name="index_source" value="cached"/><param name="out_format" value="interval"/><output name="out_file1" file="extract_genomic_dna_out3.interval" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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