details: http://www.bx.psu.edu/hg/galaxy/rev/411b53d32b78 changeset: 2975:411b53d32b78 user: Kelly Vincent <kpvincent@bx.psu.edu> date: Fri Nov 06 09:57:05 2009 -0500 description: Fixed BWA wrapper tests (inputs need to be specified fastqsanger because there's no longer a sniff method for that type) diffstat: tools/sr_mapping/bwa_wrapper.xml | 18 +++++++++--------- 1 files changed, 9 insertions(+), 9 deletions(-) diffs (70 lines): diff -r 12518f99a2a7 -r 411b53d32b78 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Fri Nov 06 00:25:02 2009 -0500 +++ b/tools/sr_mapping/bwa_wrapper.xml Fri Nov 06 09:57:05 2009 -0500 @@ -161,7 +161,7 @@ <param name="refGenomeSource" value="indexed" /> <param name="indices" value="phiX" /> <param name="sPaired" value="single" /> - <param name="input1" value="bwa_wrapper_in1.fastq" /> + <param name="input1" value="bwa_wrapper_in1.fastq" ftype="fastqsanger" /> <param name="source_select" value="pre_set" /> <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out0.sam" ftype="sam" /> @@ -171,7 +171,7 @@ <param name="refGenomeSource" value="history" /> <param name="ownFile" value="phiX.fa" /> <param name="sPaired" value="single" /> - <param name="input1" value="bwa_wrapper_in0.fastq" /> + <param name="input1" value="bwa_wrapper_in0.fastq" ftype="fastqsanger" /> <param name="source_select" value="pre_set" /> <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out0b.sam" ftype="sam" /> @@ -181,7 +181,7 @@ <param name="refGenomeSource" value="indexed" /> <param name="indices" value="phiX" /> <param name="sPaired" value="single" /> - <param name="input1" value="bwa_wrapper_in2.fastq" /> + <param name="input1" value="bwa_wrapper_in2.fastq" ftype="fastqsanger" /> <param name="source_select" value="full" /> <param name="maxEditDist" value="0" /> <param name="fracMissingAligns" value="0.04" /> @@ -208,8 +208,8 @@ <param name="refGenomeSource" value="indexed" /> <param name="indices" value="phiX" /> <param name="sPaired" value="paired" /> - <param name="input1" value="bwa_wrapper_in3.fastq" /> - <param name="input2" value="bwa_wrapper_in4.fastq" /> + <param name="input1" value="bwa_wrapper_in3.fastq" ftype="fastqsanger" /> + <param name="input2" value="bwa_wrapper_in4.fastq" ftype="fastqsanger" /> <param name="source_select" value="full" /> <param name="maxEditDist" value="0" /> <param name="fracMissingAligns" value="0.04" /> @@ -236,7 +236,7 @@ <param name="refGenomeSource" value="indexed" /> <param name="indices" value="phiX" /> <param name="sPaired" value="single" /> - <param name="input1" value="bwa_wrapper_in1.fastq" /> + <param name="input1" value="bwa_wrapper_in1.fastq" ftype="fastqsanger" /> <param name="source_select" value="full" /> <param name="maxEditDist" value="0" /> <param name="fracMissingAligns" value="0.04" /> @@ -263,8 +263,8 @@ <param name="refGenomeSource" value="indexed" /> <param name="indices" value="phiX" /> <param name="sPaired" value="paired" /> - <param name="input1" value="bwa_wrapper_in5.fastq" /> - <param name="input2" value="bwa_wrapper_in6.fastq" /> + <param name="input1" value="bwa_wrapper_in5.fastq" ftype="fastqsanger" /> + <param name="input2" value="bwa_wrapper_in6.fastq" ftype="fastqsanger" /> <param name="source_select" value="full" /> <param name="maxEditDist" value="0" /> <param name="fracMissingAligns" value="0.04" /> @@ -285,7 +285,7 @@ <param name="maxOccurPairing" value="100000" /> <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out4.sam" ftype="sam" /> - </test> + </test> </tests> <help>