Mercurial > repos > jeltje > samtools_1_18_mpileup
changeset 0:41c4eb01c566 draft
Uploaded
| author | jeltje |
|---|---|
| date | Mon, 12 Jan 2015 14:31:17 -0500 |
| parents | |
| children | afb57162f902 |
| files | samtools_mpileup.xml tool_dependencies.xml |
| diffstat | 2 files changed, 38 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_mpileup.xml Mon Jan 12 14:31:17 2015 -0500 @@ -0,0 +1,32 @@ +<tool id="samtools_0_1_18mpileup" name=mpileup" version="1.0.0"> + <requirements> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <description>runs basic mpileup on input control and tumor files</description> + <command>samtools mpileup -q 1 -B "$index" "$bamc" "$bamt"> "$output1" + </command> + <inputs> + <param name="bamc" type="data" format="bam" label="BAM file (control)" /> + <param name="bamt" type="data" format="bam" label="BAM file (tumor)" /> + <param name="index" type="select"> + <options from_data_table="picard_index" /> + </param> + </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 mpileup command of samtools 0.1.18 +with flags -q 1 -B + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 12 14:31:17 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>