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<tool id="cnvkit_tool" name="CNVkit Tool">
<description>Infer copy number variants and alterations using CNVkit</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 the CNVkit pipeline on one or more tumor or germline samples, using zero or
more normal samples to construct a reference, along with a BED file indicating the baits
used in hybrid capture for sequencing. Returns the constructed reference and the segmented
copy number ratio values as two tables.
</help>
</tool>
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