Mercurial > repos > chrisd > resistome_analyzer

view resistome_analyzer.xml @ 1:c9fbf44a96f7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/resistomeanalyzer commit 8ae28ea5f8b137ff7403efbb968152aa6aae22bf
author chrisd
date Tue, 11 Oct 2016 03:47:35 -0400
parents 6e3417efcef3
children
line wrap: on
line source

<tool id="resistome_analyzer" name="ResistomeAnalyzer" version="0.1.0">
    <description>A simple tool for analyzing the resistome of metagenomic sequence data</description>
    <requirements>
	<requirement type="package" version="0.1">resistomeanalyzer</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
	resistome
	  -ref_fp $reference
	  -annot_fp $annotation
	  -sam_fp $sam
	  -gene_fp $gene
	  -mech_fp $mech
	  -class_fp $class
	  -group_fp $group
	  -t $threshold
    ]]></command>
    <inputs>
	<param type="data" name="reference" format="fasta" label="Reference sequence" />
	<param type="data" name="sam" format="sam" label="SAM file" />
	<param type="data" name="annotation" format="csv" label="Annotation file" />
	<param name="threshold" type="integer" label="Gene fraction threshold"
               value="0" min="0" max="100" />
    </inputs>
    <outputs>
	<data name="gene" format="tabular" />
	<data name="mech" format="tabular" />
	<data name="class" format="tabular" />
	<data name="group" format="tabular" />
    </outputs>
    <citations>
    </citations>
</tool>