Mercurial > repos > drosofff > cherry_pick_fasta
view cherry_pick_fasta.xml @ 1:f7684171dab3 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit b6de14061c479f0418cd89e26d6f5ac26e565a07
author | drosofff |
---|---|
date | Wed, 09 Nov 2016 11:31:12 -0500 |
parents | c7a0ec8263b4 |
children |
line wrap: on
line source
<tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="0.9.0"> <description>with header satisfying a query string</description> <command interpreter="python">cherry_pick_fasta.py --input $input --query-string "$query" --output $output </command> <inputs> <param name="query" type="text" size="30" value="" label="Select sequences with this string in their header" help="exemple: gi|40557596"> <sanitizer> <valid initial="string.printable"> <remove value="""/> <remove value="\"/> </valid> <mapping initial="none"> <add source=""" target="\""/> <add source="\" target="\\"/> </mapping> </sanitizer> </param> <param format="fasta" label="Source file" name="input" type="data" /> </inputs> <outputs> <data name="output" format="fasta" label="${tool.name} on ${on_string} including '${query.value}' in header" /> </outputs> <tests> <test> <param ftype="fasta" name="input" value="input.fa" /> <param name="query" value="gi|81971654" /> <output name="output" ftype="fasta" file="output.fa" /> </test> </tests> <help> **What it does** This tool retrieves nucleotide/peptide sequences from a fasta file whose headers match a given query string. It is Copyright © 2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_. .. _CNRS and University Pierre et Marie Curie: http://www.upmc.fr/en/index.html .. _MIT license: http://opensource.org/licenses/MIT </help> </tool>