1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/a6141e135830/ changeset: r5114:a6141e135830 user: natefoo date: 2011-02-23 19:54:06 summary: Update bwa_wrapper to use the test data repository. bwa_color_wrapper will need to be done once the test data repository is updated to contain the data it uses. affected #: 1 file (258 bytes)
--- a/tools/sr_mapping/bwa_wrapper.xml Wed Feb 23 11:56:16 2011 -0500 +++ b/tools/sr_mapping/bwa_wrapper.xml Wed Feb 23 13:54:06 2011 -0500 @@ -139,8 +139,7 @@ python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out1.u.sam bwa_wrapper_out1.sam --><param name="refGenomeSource" value="indexed" /> - <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> - <param name="indices" value="/galaxy/data/phiX/bwa_index/phiX.fa" /> + <param name="indices" value="phiX" /><param name="sPaired" value="single" /><param name="input1" value="bwa_wrapper_in1.fastqsanger" ftype="fastqsanger" /><param name="source_select" value="pre_set" /> @@ -195,8 +194,7 @@ python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out3.u.sam bwa_wrapper_out3.sam --><param name="refGenomeSource" value="indexed" /> - <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> - <param name="indices" value="/galaxy/data/phiX/bwa_index/phiX.fa" /> + <param name="indices" value="phiX" /><param name="sPaired" value="paired" /><param name="input1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" /><param name="input2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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