comparison spades_header_fixer.xml @ 0:f57f28bdd39b draft default tip

"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
author nml
date Thu, 19 Dec 2019 10:07:39 -0500
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-1:000000000000 0:f57f28bdd39b
1 <tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.1">
2 <description>Fixes Spades Fasta ids</description>
3 <requirements>
4 <requirement type="package" version="4.7.0">sed</requirement>
5 </requirements>
6 <command >sed -r "s/>NODE(_[0-9]+)_(.*)/>${input.element_identifier}\1 \2/g" $input >$output</command>
7 <inputs>
8 <param name="input" type="data" format="fasta" label="Fix these fasta headers"/>
9 </inputs>
10 <outputs>
11 <data name="output" format="fasta"/>
12 </outputs>
13 <tests>
14 <test>
15 <param name="input" value="spades_before.fasta" />
16 <output name="output" file="spades_header_fixed.fasta" ftype="fasta"/>
17 </test>
18 </tests>
19
20 <help><![CDATA[
21 SPAdes fasta header fixer
22 =======
23
24 The SPAdes header fixer tool replaces the default value of NODE from SPAdes fasta header(s) to either a filename or a collection identifier.
25 ]]></help>
26
27 <citations>
28 <citation type="bibtex">@ARTICLE{a1,
29 title = {SPAdes fasta header fixer},
30 author = {Philip Mabon},
31 url = {https://github.com/phac-nml/galaxy_tools}
32 }
33 }</citation>
34 </citations>
35 </tool>