view graph_coverage_multi_png.xml @ 1:7bcef9bf4f18 draft default tip

Uploaded wrapper

<tool id="get_cov_graph" name="get graph of coverage depth" version="1.16">
  <description>
    From coverage file (after samtools depth with "-a -d 0" option), get graph for each reference used in the alignment.
  </description>
  <requirements>
    <requirement type="package" version="4.1">r</requirement>
    <requirement type="package" version="0.8.9">r-reshape</requirement>
    <requirement type="package" version="3.3.6">r-ggplot2</requirement>
    <requirement type="package" version="1.4.1">r-stringr</requirement>
    <requirement type="package" version="2.3">r-gridextra</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[
    mkdir -p graph_cov;
    Rscript '$__tool_directory__/graph_coverage_multi_png.R' "$depth_file" graph_cov/coverage_graph.png
  ]]></command>
  <inputs>
    <param name="depth_file" type="data" format="tabular" label="Depth file" help="Output from samtools depth command"/>
  </inputs>
  <outputs>
    <collection name="output" type="list" label="Unknown number of graph files" >
      <discover_datasets pattern="__designation_and_ext__" directory="graph_cov" ext="png"/>
    </collection>
  </outputs>
  <help>
  <![CDATA[

Homemade script to get one coverage graphe by reference of alignment.
If you have more than 8 reference in reference file, others files will be created.
  ]]>
  </help>
</tool>