Commit 01566894 authored by Philip Mabon's avatar Philip Mabon

Merge branch 'development' into 'development'

Snvphyl reporter wrapper

The snvphyl reporter galaxy wrapper. This first version only checks bam files.

See merge request !4
parents 8c66b21d 8e049371
<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"}}
\ No newline at end of file
<?xml version="1.0"?>
<tool_dependency>
<package name="snvphyl" version="1.3.5">
<repository name="package_snvphyl" owner="phil"/>
</package>
</tool_dependency>
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