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<tool id="CloudMap Config" name="Generate a species configuration file">
  <description>for use with CloudMap.</description>
  <requirements>
    <requirement type="package" version="3.4.1">python3</requirement>
    <requirement type="package" version="0.1.3_9af04e0e9125">MiModD</requirement>
  </requirements>
  <command>
    mimodd cm_seqdict $ifile -o $outputfile
  </command>

  <inputs>
    <param name="ifile" type="data" format="vcf" label="vcf input file" />
  </inputs>

  <outputs>
    <data name="outputfile" format="tabular" label="Sequence Dictionary for CloudMap from ${on_string}"/>
  </outputs>

  <help>
.. class:: infomark

   **What it does**

The purpose of this tool is solely to provide compatibility with the external **CloudMap** *Variant Discovery Mapping* and *Hawaiian Variant Mapping* tools.

From a VCF file, the tool extracts the chromosome names and sizes and reports them in the **CloudMap** *species configuration file* format.
Such a file is required as input to the **CloudMap** mapping tools, if you are working with a species other than the natively supported ones (i.e., other than C.elegans or A. thaliana for the current version of CloudMap).
   
  </help>
</tool>