view coverage_sampler.xml @ 37:520bc487403d draft

planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 660fc35f51cce194be9d5f050f7353b47ab23fd1-dirty

<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 levels alignments were taken at
    Iteration	The iteration at each 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 amount of alignments associated with the reference sequence at the current sample level

------

**Development**

Development is being done on github_

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

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