Mercurial > repos > scisjnu123 > test
changeset 25:765d954df8bf draft
Uploaded
| author | scisjnu123 |
|---|---|
| date | Fri, 27 Sep 2019 08:55:46 -0400 |
| parents | d6b1131dd9f2 |
| children | 81a543035990 |
| files | samtools_sort/samtools_sort.xml |
| diffstat | 1 files changed, 2 insertions(+), 20 deletions(-) [+] |
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--- a/samtools_sort/samtools_sort.xml Fri Sep 27 08:42:59 2019 -0400 +++ b/samtools_sort/samtools_sort.xml Fri Sep 27 08:55:46 2019 -0400 @@ -6,7 +6,7 @@ <expand macro="requirements"></expand> <expand macro="stdio"></expand> <expand macro="version_command"></expand> - <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command> + <command>samtools sort "${input1}" "${output1}"</command> <inputs> <param name="input1" type="data" format="bam" label="BAM File" /> <param name="sort_mode" type="select" label="Sort by "> @@ -17,24 +17,6 @@ <outputs> <data name="output1" format="bam" /> </outputs> - <tests> - <test> - <param name="input1" value="1.bam" ftype="bam" /> - <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/> - </test> - <test> - <param name="input1" value="1.bam" ftype="bam" /> - <param name="sort_mode" value="-n"/> - <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/> - </test> - </tests> - <help> - -**What it does** - -This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order. - - - </help> + <expand macro="citations"></expand> </tool>