Commit 5601ba14 authored by Mariam's avatar Mariam

Uploading snvphyl_reporter galaxy wrapper

parent ad3a47ad
<tool id="snvphyl_reporter" name="Snvphyl Reporter" version="1.0">
<description>Runs Snvphyl reporter</description>
<requirements>
<requirement type="package" version="1.3.5">snvphyl</requirement>
</requirements>
<command interpreter="perl">
/\$VCF2PSEUDO/reporter.pl --step bam_quality_data --output $output
#for $f in $input.keys#
--bam "$f=$input[$f]"
#end for
</command>
<inputs>
<param name="input" type="data_collection" lable="Bam files Collection" help="Please enter a list collection of bam files" optional="false" collection_type="list" />
</inputs>
<outputs>
<data name="output" format="txt" label="Reporter Output" />
</outputs>
<tests>
<test>
<param name="input">
<collection type="list">
<element name="sample1" value="sample1.bam" />
<element name="sample2" value="sample2.bam" />
<element name="sample3" value="sample3.bam" />
</collection>
</param>
<output name="output" file="bam_reporter_out.txt" />
</test>
</tests>
<help>
This tool runs the SNVPhyl Reporter pipeline.
</help>
</tool>
{"bam_stats":{"warn_mapping_threshold":90,"Common problems":[["Insufficient amount of sequencing data","Sample contamination","Imporperly identified/labelled samples","Poor reference strain used"]],"failed_mapping_threshold":80,"Problem strains":[],"min_depth":"15","status":"PASSED","Common solutions":[["Top up the sequencing data for the poorly mapped isolates","Remove isolates that are mapping poorly from the analysis","Ensure the samples are identified and labelled correctly","Select a different reference strain to map to"]]},"reference":{"size_from_bam":"48502"}}
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<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.5">
<repository changeset_revision="58ff556e1be9" name="package_snvphyl" owner="phil" toolshed="http://galaxy-toolshed.corefacility.ca"/>
</package>
</tool_dependency>
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