Mercurial > repos > nml > spades_fasta_header_fixer
view spades_header_fixer.xml @ 1:4a80a8ffb288 draft
planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
author | nml |
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date | Fri, 02 Sep 2022 20:18:41 +0000 |
parents | f57f28bdd39b |
children | 2cc9e69419d2 |
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<tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.2+galaxy0"> <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>