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author triasteran
date Tue, 22 Feb 2022 16:14:23 +0000
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<tool id="bam2bigwig" name="Convert Bam to BigWig" version="0.1.0" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="0.18.0">pysam</requirement>
        <requirement type="package" version="2.30.0">bedtools</requirement>
        <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>        
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       python3 '$__tool_directory__/bam_to_bigwig.py3' '$input1' --outfile=$output1
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="bam" />
    </inputs>
    <outputs>
        <data name="output1" format="bigwig" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="file.bam"/>
            <output name="output1" file="out.bigwig"/>
        </test>
    </tests>
    <help>
      <![CDATA[
Convert BAM files to BigWig file format in a specified region.

Usage:
    bam_to_wiggle.py <BAM file> <YAML config> --outfile=<output file name> ]]>
    </help>
    <citations>
        <citation type="bibtex">
           @misc{githubbam_to_bigwig,
  author = {Audrey},
  year = {2022},
  title = {bam_to_bigwig},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/triasteran/RiboGalaxy_tools}, }
        </citation>
    </citations>
</tool>