Mercurial > repos > nml > spades_fasta_header_fixer
view spades_header_fixer.xml @ 2:2cc9e69419d2 draft default tip
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit c32ec4a9284ec939d001bd7d7d551c15feaa5333
author | nml |
---|---|
date | Mon, 07 Nov 2022 23:41:29 +0000 |
parents | 4a80a8ffb288 |
children |
line wrap: on
line source
<tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.2+galaxy1"> <description>Fixes Spades Fasta ids</description> <requirements> <requirement type="package" version="4.7.0">sed</requirement> </requirements> <command >sed -r "s/>NODE(_[0-9]+)_(.*)|>contig/>${input.element_identifier}\1_\2/g" $input >$output</command> <inputs> <param name="input" type="data" format="fasta" label="Fix these fasta headers"/> </inputs> <outputs> <data name="output" format="fasta"/> </outputs> <tests> <test> <param name="input" value="spades_before_1.fasta" /> <output name="output" file="spades_header_fixed_1.fasta" ftype="fasta"/> </test> <test> <param name="input" value="spades_before_2.fasta" /> <output name="output" file="spades_header_fixed_2.fasta" ftype="fasta"/> </test> </tests> <help><![CDATA[ SPAdes fasta header fixer ======= The SPAdes header fixer tool replaces the default value of NODE from SPAdes fasta header(s) to either a filename or a collection identifier. ]]></help> <citations> <citation type="bibtex">@ARTICLE{a1, title = {SPAdes fasta header fixer}, author = {Philip Mabon}, url = {https://github.com/phac-nml/galaxy_tools} } }</citation> </citations> </tool>