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"planemo upload for repository https://github.com/bvalot/panISa commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb"
author | bvalot |
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date | Thu, 16 Jun 2022 12:37:30 +0000 |
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<tool id="panisa2_wrapper" name="PanISa: IS search" version="0.1.6"> <description>Search integrative element (IS) insertion on a genome using BAM alignment</description> <requirements> <requirement type="package" version="0.1.6">panisa</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" /> </stdio> <version_command>panISa.py -v</version_command> <command> panISa.py #if str($quality) -q $quality #end if #if str($minimun) -m $minimun #end if #if str($size) -s $size #end if #if str($percentage) -p $percentage #end if '$bam' > '$output' </command> <inputs> <param name="bam" type="data" format="bam" label="Alignment result" help="Bam format" /> <param name="quality" type="integer" value="20" optional="true" label="Minimun alignment quality value to conserve a clipped" /> <param name="minimun" type="integer" value="5" optional="true" label="Minimun number of clipped reads to look at IS on a position" /> <param name="size" type="integer" value="20" optional="true" label="Maximun size of direct repeat region" /> <param name="percentage" type="float" value="0.8" optional="true" label="Minimum percentage of same base to create consensus" /> </inputs> <outputs> <data name="output" format="tabular" label="panISa on ${bam.name}"> <!-- <actions> --> <!-- <action name="column_names" type="metadata" default="Chromosome,End position,End clipped reads,Direct repeats,Start position,Start clipped reads,Inverted repeats,Left sequence,Right sequence" /> --> <!-- </actions> --> </data> </outputs> <tests> <test expect_num_outputs="1"> <param name="bam" value="input.bam" /> <output name="output" file="panisa.txt" ftype="tabular" /> </test> </tests> <help> **What it does** Search integrative element (IS) insertion on a genome using BAM alignment. **License and citation** This Galaxy tool is Copyright © 2018 `B. Valot` and is released under the `GPL3 license`. PanISa program was publised : Treepong, P., Guyeux, C., Meunier, A., Couchoud, C., Hocquet, D. et Valot, B. (2018). PanISa : Ab initio detection of insertion sequences in bacterial genomes from short read sequence data. Bioinformatics. </help> <citations> <citation type="doi">10.1093/bioinformatics/bty479</citation> </citations> </tool>