view spades_header_fixer.xml @ 0:f57f28bdd39b draft

"planemo upload for repository commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
author nml
date Thu, 19 Dec 2019 10:07:39 -0500
children 4a80a8ffb288
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<tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.1">
	<description>Fixes Spades Fasta ids</description>
      <requirement type="package" version="4.7.0">sed</requirement>
	<command >sed -r "s/>NODE(_[0-9]+)_(.*)/>${input.element_identifier}\1 \2/g" $input >$output</command>
		<param name="input" type="data" format="fasta" label="Fix these fasta headers"/>
		<data name="output" format="fasta"/>
         <param name="input" value="spades_before.fasta" />
         <output name="output" file="spades_header_fixed.fasta" ftype="fasta"/>

    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.

        <citation type="bibtex">@ARTICLE{a1,
            title = {SPAdes fasta header fixer},
            author = {Philip Mabon},
            url = {}