<tool id="CSAW" name="CSAW" version="0.1.0">
  
  <requirements>
    <requirement type="package" version="1.12.0">bioconductor-csaw</requirement>
    <requirement type="package" version="1.20.0">r-getopt</requirement>
    <requirement type="package" version="1.10.4">r-data.table</requirement>
    <requirement type="package" version="1.2.0">r-stringr</requirement>
    <requirement type="package" version="1.12.0">bioconductor-biocparallel</requirement>
<requirement type="package" version="1.8.0">bioconductor-summarizedexperiment</requirement>
<requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
<requirement type="package" version="1.30.0">bioconductor-genomicranges</requirement>
<requirement type="package" version="1.14.0">bioconductor-genomeinfodb</requirement>
<requirement type="package" version="2.12.0">bioconductor-iranges</requirement>
<requirement type="package" version="0.16.0">bioconductor-s4vectors</requirement>
<requirement type="package" version="0.24.0">bioconductor-biocgenerics</requirement>
<requirement type="package" version="1.30.0">bioconductor-rsamtools</requirement>
<requirement type="package" version="2.46.0">bioconductor-biostrings</requirement>
<requirement type="package" version="0.18.0">bioconductor-xvector</requirement>
  </requirements>
  
  <command detect_errors="exit_code"><![CDATA[
Rscript $__tool_directory__/csaw.R $inputs $output
    ]]></command>
  
  <inputs>
    <param type="data" name="inputs" format="bam" multiple="True" />
  </inputs>
  
  <outputs>
    <data name="output" format="txt"/>
    <collection name="countTables" type="list">
      <discover_datasets pattern="(?P&1t;name&gt;.+)\.tsv$" format="tabular"  visible="false" />
    </collection>
  </outputs>
  
  <tests>
    <test>
      <param name="inputs" value="ENCFF027UTM.bam,ENCFF027UTM_1.bam"/>
      <output name="output" file="csaw_results"/>
    </test>
  </tests>
  
  <help><![CDATA[
        Write the tool help section here.
    ]]></help>
  
  <citations>
    <citation type="bibtex">
      @misc{github01_mismatch_removal,
      author = {LastTODO, FirstTODO},
      year = {TODO},
      title = {01_mismatch_removal},
      publisher = {GitHub},
      journal = {GitHub repository},
      url = {https://github.com/dktanwar/Galaxy_Tools/tree/master/01_mismatch_removal},
      }</citation>
  </citations>
</tool>