Mercurial > repos > nml > spades_fasta_header_fixer
comparison spades_header_fixer.xml @ 0:f57f28bdd39b draft
"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 6d09bbbbade6035f9acc0345bee9f4bb71cfc102"
author | nml |
---|---|
date | Thu, 19 Dec 2019 10:07:39 -0500 |
parents | |
children | 4a80a8ffb288 |
comparison
equal
deleted
inserted
replaced
-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> |