<tool id="gene_fraction" name="Coverage Sampler" version="0.1.0">
    <description>A simple tool for calculating the amount of a gene that is covered by a sample of alignments</description>
    <requirements>
	<requirement type="package" version="0.1">coverage_sampler</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
	csa
	  -ref_fp $reference
	  -sam_fp $sam
	  -min $min
	  -max $max
	  -t $threshold
	  -skip $skip
	  -samples $samples
	  -out_fp $output
    ]]></command>
    <inputs>
	<param type="data" name="reference" format="fasta" label="Reference sequence" />
	<param type="data" name="sam" format="sam" label="SAM file" />
	<param name="min" type="integer" label="Starting sample level"
	       value="1" min="1" max="100" help="(-min)" />
	<param name="max" type="integer" label="Ending sample level"
	       value="1" min="1" max="100" help="(-max)" />
	<param name="threshold" type="integer" label="Gene fraction threshold"
	       value="0" min="0" max="100" help="(-t)" />
	<param name="skip" type="integer" label="Amount of sample levels to skip"
	       value="1" min="1" max="100" help="(-skip)" />
	<param name="samples" type="integer" label="Iterations per sample level"
	       value="1" min="1" max="100" help="(-samples)" />
    </inputs>
    <outputs>
	<data name="output" format="tabular" />
    </outputs>
    <tests>
      <test>
          <param name="reference" value="ref.fa"/>
      	  <param name="sam" value="sampe.sam"/>
	  <param name="min" value="100"/>
	  <param name="max" value="100"/>
	  <param name="threshold" value="50"/>
	  <param name="skip" value="5"/>
	  <param name="samples" value="1"/>
      	  <output name="output" file="csa_result" ftype="tabular"/>
      </test>
      <test>
	  <param name="reference" value="ref.fa"/>
          <param name="sam" value="sampe.sam"/>
          <param name="min" value="100"/>
          <param name="max" value="100"/>
          <param name="threshold" value="80"/>
          <param name="skip" value="5"/>
          <param name="samples" value="1"/>
          <output name="output" file="csa_no_result" ftype="tabular"/>
      </test>
    </tests>
    <help><![CDATA[

**Coverage sampler**

Coverage sampler is a simple tool for calculating the amount of a gene that is covered by a sample of alignments. The tool takes
in as input a fasta and alignment file. The output of this program is a tab delimited text file describing the fraction of each gene
that was covered from a random sampling of alignments.

------

**Options**

    -min     INT    Starting level to sample reads from (level is in percent)

    -max     INT    Ending level to sample reads from (level is in percent)

    -skip    INT    Number of levels to skip

    -samples  INT    Number of iterations per sample level

    -t       INT    Gene fraction threshold (only genes with a gene fraction greater than this threshold are output)

------

**Output**

A tab delimited text file with the following columns::

    Level		The sampling level alignments were taken at
    Iteration		The iteration number of the current sample level
    Gene Id		The reference name having a gene fraction greater than threshold
    Gene Fraction	The gene fraction for the current reference sequence (in percent)
    Hits		The number of alignments associated with the reference sequence

------

**Development**

Development is being done on github_

.. _github: https://github.com/cdeanj/coverage_sampler

 ]]></help>
    <citations>
    </citations>
</tool>