Mercurial > repos > bgruening > deeptools_test_new_python_stack
diff bamPEFragmentSize.xml @ 0:b2886915ce68 draft default tip
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| author | bgruening |
|---|---|
| date | Tue, 10 Feb 2015 03:21:34 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamPEFragmentSize.xml Tue Feb 10 03:21:34 2015 -0500 @@ -0,0 +1,56 @@ +<tool id="deeptools_bamPEFragmentSize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0"> + <description>Given a BAM file it samples several regions to estimate the paird-end fragment length</description> + <expand macro="requirements" /> + <expand macro="stdio" /> + <macros> + <token name="@BINARY@">bamPEFragmentSize</token> + <import>deepTools_macros.xml</import> + </macros> + <command> +<![CDATA[ + bamPEFragmentSize + @THREADS@ + -bai ${bamInput.metadata.bam_index} + #if $histogram: + --histogram ./hist.png + #end if + '$bamInput' + > $outfile + && + mv ./hist.png $histogram_outfile +]]> + </command> + <inputs> + <param name="bamInput" format="bam" type="data" label="BAM file" + help="The BAM file must be sorted."/> + <param name="histogram" type="boolean" truevalue="--histogram" falsevalue="" + label="Get the distribion of fragment length as histogram" + help="(--histogram)"/> + </inputs> + <outputs> + <data name="outfile" format="txt"/> + <data name="histogram_outfile" format="png"> + <filter>histogram is True</filter> + </data> + </outputs> + <tests> + <test> + <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" /> + <param name="histogram" value="True" /> + <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" /> + <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Given a BAM file it samples several regions to estimate the paird-end fragment length. + +----- + +@REFERENCES@ +]]> + </help> + <expand macro="citations" /> +</tool>