Mercurial > repos > wolma > mimodd

<tool id="fileinfo" name="Retrieve File Information" version="0.1.7.0">
  <description>for supported data formats.</description>
  <macros>
    <import>toolshed_macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command>mimodd version -q</version_command>
  <command>
    mimodd info "$ifile" -o "$outputfile" --verbose --oformat $oformat
  </command>

  <inputs>
    <param name="ifile" type="data" format="bam,sam,vcf,bcf,fasta" label="input file" />
    <param name="oformat" type="select" label="output format">
        <option value="txt">text</option>
        <option value="html">html</option>
    </param>
  </inputs>

  <outputs>
    <data name="outputfile" format="txt" label="Sample Info on ${on_string}">
      <change_format>
	    <when input="oformat" value="html" format="html"/>
      </change_format>
    </data>
  </outputs>

<help>
.. class:: infomark

   **What it does**

The tool inspects the input file and generates a report summarizing its contents.

It autodetects and works with most file formats produced by MiModD, i.e., **SAM / BAM, vcf / bcf and fasta**, and produces a standardized report for all of them.

</help>
</tool>
author	Wolfgang Maier
date	Tue, 22 Sep 2015 22:36:41 +0200
parents	85214e4428fd
children	d79fe626c6fd