view coverage_sampler.xml @ 24:750a09c9cca2 draft

planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit b3a650c3506c27e7b80069dd88d87fa11c5369b9-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:

Column	Description
Level	The sampling level alignments were taken at
Iteration	The ith iteration of the current sampling level
Gene Id	The reference sequence having a gene fraction greater than threshold
Gene Fraction	The overall fraction of the gene that was covered from the sample of alignments
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>