Mercurial > repos > etal > cnvkit
changeset 0:86dfb8210840 draft default tip
Uploaded
| author | etal |
|---|---|
| date | Sun, 21 Sep 2014 14:11:10 -0400 |
| parents | |
| children | |
| files | cnvExample.xml |
| diffstat | 1 files changed, 40 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cnvExample.xml Sun Sep 21 14:11:10 2014 -0400 @@ -0,0 +1,40 @@ +<tool id="cnvkit_ex_1" name="CNVkit Example"> + <description>this is the description</description> + <command interpreter="python"> +cnvkit.py batch +#for i in $samplebams#${i} #end for# +-n +#for j in $normalbams#${j} #end for# +-t "$targetbed" --output-reference "$outputref" +&& +cnvkit.py export seg *.cns -o "$outputseg" + </command> + <inputs> + <param format="bam" name="samplebams" type="data" label="Sample BAM file(s)" multiple="true"/> + <param format="bam" name="normalbams" type="data" label="Normal BAM file(s)" multiple="true" optional="true"/> + <param format="bed" name="targetbed" type="data" label="Baits BED file"/> + </inputs> + <outputs> + <data format="tabular" name="outputref" /> + <data format="tabular" name="outputseg" /> + </outputs> + + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + + <tests> + <test> + <param name="samplebams" value="test.bam"/> + <param name="targetbed" value="test.bed"/> + <output name="out_file1" file="test_cnvkit_output.txt"/> + </test> + </tests> + + <help> +This tool runs segmentation on a CNVkit CNR file. + </help> + +</tool>