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Fixed BWA wrapper tests (inputs need to be specified fastqsanger because there's no longer a sniff method for that type)

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Kelly Vincent
2009-11-06 09:57:05 -05:00
parent 905a6e503b
commit 39f0958f35
1 changed files with 9 additions and 9 deletions
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tools/sr_mapping/bwa_wrapper.xml
+9 -9
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@@ -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>