Mercurial > repos > nml > spades_fasta_header_fixer

comparison spades_header_fixer.xml @ 1:4a80a8ffb288 draft

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planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3051c6185128618cb9f137a10f45c248f6a6097f
author nml
date Fri, 02 Sep 2022 20:18:41 +0000
parents f57f28bdd39b
children 2cc9e69419d2
comparison
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0:f57f28bdd39b 1:4a80a8ffb288
1 <tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.1"> 1 <tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.2+galaxy0">
2 <description>Fixes Spades Fasta ids</description> 2 <description>Fixes Spades Fasta ids</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.7.0">sed</requirement> 4 <requirement type="package" version="4.7.0">sed</requirement>
5 </requirements> 5 </requirements>
6 <command >sed -r "s/>NODE(_[0-9]+)_(.*)/>${input.element_identifier}\1 \2/g" $input >$output</command> 6 <command >sed -r "s/>NODE(_[0-9]+)_(.*)|>contig/>${input.element_identifier}\1 \2/g" $input >$output</command>
7 <inputs> 7 <inputs>
8 <param name="input" type="data" format="fasta" label="Fix these fasta headers"/> 8 <param name="input" type="data" format="fasta" label="Fix these fasta headers"/>
9 </inputs> 9 </inputs>
10 <outputs> 10 <outputs>
11 <data name="output" format="fasta"/> 11 <data name="output" format="fasta"/>
12 </outputs> 12 </outputs>
13 <tests> 13 <tests>
14 <test> 14 <test>
15 <param name="input" value="spades_before.fasta" /> 15 <param name="input" value="spades_before_1.fasta" />
16 <output name="output" file="spades_header_fixed.fasta" ftype="fasta"/> 16 <output name="output" file="spades_header_fixed_1.fasta" ftype="fasta"/>
17 </test>
18 <test>
19 <param name="input" value="spades_before_2.fasta" />
20 <output name="output" file="spades_header_fixed_2.fasta" ftype="fasta"/>
17 </test> 21 </test>
18 </tests> 22 </tests>
19 23
20 <help><![CDATA[ 24 <help><![CDATA[
21 SPAdes fasta header fixer 25 SPAdes fasta header fixer