view get_cov_stats.xml @ 0:2e05d9335bae draft

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<tool id="get_cov_stats" name="get statistics from bam file" version="1">
  <description>
    From bam file, get some statistics
  </description>
  <requirements>
    <requirement type="package" version="3.6.0">r</requirement>
    <requirement type="package" version="1.14">samtools</requirement>
    <requirement type="package" version="3.7.12">python</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[
    python '$__tool_directory__/get_cov_stats.py' 
      -bam "$bamfile" 
      #if $typeofreads.p_or_s == "paired":
        -p
      #end if
      > "$output"
  ]]></command>
  <inputs>
    <param name="bamfile" type="data" format="bam" label="Bam file" help="Bam file of an aligment"/>
    <conditional name="typeofreads">
      <param name="p_or_s" type="select" label="Read option">
        <option value="single" selected="True">Single-end</option>
        <option value="paired">Paired-end</option>
      </param>
    </conditional>
  </inputs>
  <outputs>
    <data format="txt" name="output" label="${tool.name} on ${on_string}"/>
  </outputs>
  <help>
  <![CDATA[

Homemade script to get some statistics about and bam file.

  ]]>
  </help>
</tool>