Mercurial > repos > jeltje > samtools_0_1_18_flagstat
changeset 0:a381e8c76e58 draft
Uploaded
| author | jeltje |
|---|---|
| date | Fri, 09 Jan 2015 18:40:34 -0500 |
| parents | |
| children | b469f90740f8 |
| files | samtools_flagstat.xml tool_dependencies.xml |
| diffstat | 2 files changed, 33 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_flagstat.xml Fri Jan 09 18:40:34 2015 -0500 @@ -0,0 +1,27 @@ +<tool id="samtools_0_1_18_flagstat" name="flagstat" version="1.0.0"> + <requirements> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <description>provides simple stats on BAM files</description> + <command>samtools flagstat "$input1" > "$output1" + </command> + <inputs> + <param name="input1" type="data" format="bam" label="BAM File" /> + </inputs> + <outputs> + <data name="output1" format="txt" /> + </outputs> +<!-- + <tests> + <test> + <param name="input1" value="unsorted.bam" ftype="bam" /> + <output name="output1" file="samtools_flagstat_out1.txt" /> + </test> + </tests> +--> + <help> + +This tool runs the flagstat command of samtools 0.1.18 to produce simple stats on a BAM file. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jan 09 18:40:34 2015 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.18"> + <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>