comparison coverage_sampler.xml @ 2:ec439b0e7512 draft default tip

planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 9982b8cd32dc6ecef17cd8c3bf16f42d8eb30d75-dirty

1:fa1aae53a2f3

<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">csa</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[

          <param name="samples" value="1"/>
          <output name="output" file="csa_no_result" ftype="tabular"/>
      </test>
    </tests>
    <help><![CDATA[
A simple tool for calculating the amount of a gene that is covered by a sample of alignments.

Program: Coverage Sampler

Contact: Chris Dean <[e-mail]>

Usage: csa [options]

Options:
    -ref_fp    STR/FILE	    	ref file path
    -sam_fp    STR/FILE	    	sam file path
    -min       INT      		starting sample level
    -max       INT	        	ending sample level
    -skip      INT	        	amount of sample levels to skip
    -t         INT	        	gene fraction threshold
    -samples   INT	        	iterations per sample level
    -out_fp    STR/FILE	    	output file path
    ]]></help>
    <citations>
    </citations>
</tool>

2:ec439b0e7512

<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[

          <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>