| Previous changeset 1:f627c4b93c55 (2014-06-20) |
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Commit message:
Uploaded |
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modified:
samtools_sort.xml |
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added:
test-data/1_sort.bam |
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| diff -r f627c4b93c55 -r 38ea74bd4054 samtools_sort.xml --- a/samtools_sort.xml Fri Jun 20 14:37:57 2014 -0400 +++ b/samtools_sort.xml Mon Jun 23 04:58:20 2014 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="samtools_sort" name="sort" version="1.0.1"> +<tool id="samtools_sort" name="sort" version="1.0.2"> <requirements> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> @@ -6,14 +6,16 @@ <command> samtools sort $sort_mode - "${input1}" "${output1}" + "${input1}" foo 2>&1 || echo "Error running samtools sort." >&2 + ; + mv foo.bam "${output1}" </command> <inputs> <param name="input1" type="data" format="bam" label="BAM File" /> <param name="sort_mode" type="select" label="Sort by "> - <option value="" selected="True">chromosomal coordinates </option> - <option value="-n">read names rather than by</option> + <option value="" selected="True">Chromosomal coordinates</option> + <option value="-n">Read names</option> </param> </inputs> <outputs> @@ -22,7 +24,7 @@ <tests> <test> <param name="input1" value="1.bam" ftype="bam" /> - <output name="output1" file="1.bam" ftype="bam" sort="True"/> + <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/> </test> </tests> <help> |
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| diff -r f627c4b93c55 -r 38ea74bd4054 test-data/1_sort.bam |
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| Binary file test-data/1_sort.bam has changed |