Mercurial > repos > bvalot > panisa
view isfinder_search.xml @ 0:349c2fbd38a0 draft default tip
"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="isfinder_search_wrapper" name="ISFinder search" version="0.1.6"> <description>Search IS homology in ISFinder from panISa output</description> <requirements> <requirement type="package" version="0.1.6">panisa</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" /> </stdio> <version_command>ISFinder_search.py -v</version_command> <command> ISFinder_search.py -r ' ' #if str($length) -l $length #end if #if str($identity) -i $identity #end if #if str($evalue) -e $evalue #end if #if str($alignment) -a $alignment #end if #for $panisa in $panisa_list: #if $panisa: '$panisa' #end if #end for #for $panisa in $panisa_list: #if $panisa: | sed -e "~s/`echo $panisa.file_name | sed -e '~s/.*\///'`/$panisa.name.replace('panISa on ', '')/" #end if #end for > '$output' 2> /dev/null </command> <inputs> <param name="panisa_list" type="data" format="tabular" multiple="true" label="Panisa result to merge" help="Panisa output in tabular format" /> <param name="length" type="integer" value="30" optional="true" label="Length of the IRR-IRL search" /> <param name="identity" type="integer" value="90" optional="true" min="0" max="100" label="Percentage of expected identity" /> <param name="evalue" type="float" value="0.001" optional="true" label="Expected max evalue" /> <param name="alignment" type="integer" value="80" optional="true" min="0" max="100" label="Percentage of expected coverage" /> </inputs> <outputs> <data name="output" format="tabular" label="${tool.name} on ${on_string}"> <!-- <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="panisa_list" ftype="tabular" value="panisa.txt" /> <output name="output" file="isfinder.txt" ftype="tabular" /> </test> </tests> <help> **What it does** Automate search integrative element (IS) homology in ISFinder from panISa output. **License and citation** This Galaxy tool is Copyright © 2018 `B. Valot` and is released under the `GPL3 license`. PanISa program was publised recently: 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>