view coverage_sampler.xml @ 16:94b6db9db63c draft

planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 0b575dcdcbeae31d97dc0334380bb18120568740-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		This parameter specifies the starting sample level for the program. For example, a min value
		of five tells the program to begin by taking five percent of alignments from the alignment file.
  
  -max		This parameter specifies the ending sample level for the program.

  -skip		This parameter specifies the amount of levels to skip between min and max. For example,
		if you specify a min value of five, a max value of 100, and a skip value of five, then 
		you would be sampling alignments in intervals of five.

  -t		This parameter specifies a threshold value. Only genes having a gene fraction greater than
		this value are provided as output.

  -samples	This parameter specifies the amount of iterations you would like to sample at. For example, 
		a sample value of five would sample each level five times.

------

**Output**

Output of this program is a tab delimited text file with following:

1  Level           The sampling level alignments were taken at

2  Iteration       The ith iteration of the current sampling level

3  Gene Id         The reference sequence having a gene fraction greater than threshold

4  Gene Fraction   The overall fraction of the gene that was covered from the sample of alignments

5  Hits            The amount of times that the reference sequence was seen from the sample of alignments

------

**Development**

Development is being done on github_

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

------

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