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comparison cherry_pick_fasta.xml @ 0:c7a0ec8263b4 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Sun, 21 Jun 2015 14:30:50 -0400
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children f7684171dab3
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1 <tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="0.9.0">
2 <description>with header satisfying a query string</description>
3 <command interpreter="python">cherry_pick_fasta.py
4 --input $input
5 --query-string "$query"
6 --output $output
7 </command>
8
9 <inputs>
10 <param name="query" type="text" size="30" value="" label="Select sequences with this string in their header" help="exemple: gi|40557596">
11 <sanitizer>
12 <valid initial="string.printable">
13 <remove value="&quot;"/>
14 <remove value="\"/>
15 </valid>
16 <mapping initial="none">
17 <add source="&quot;" target="\&quot;"/>
18 <add source="\" target="\\"/>
19 </mapping>
20 </sanitizer>
21 </param>
22 <param format="fasta" label="Source file" name="input" type="data" />
23 </inputs>
24 <outputs>
25 <data name="output" format="fasta" label="${tool.name} on ${on_string} including '${query.value}' in header" />
26 </outputs>
27 <tests>
28 <test>
29 <param ftype="fasta" name="input" value="input.fa" />
30 <param name="query" value="gi|81971654" />
31 <output name="output" ftype="fasta" file="output.fa" />
32 </test>
33 </tests>
34 <help>
35 **What it does**
36
37 This tool retrieves nucleotide/peptide sequences from a fasta file whose headers match a given query string
38
39 It is Copyright © 2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
40
41 .. _CNRS and University Pierre et Marie Curie: http://www.upmc.fr/en/index.html
42 .. _MIT license: http://opensource.org/licenses/MIT
43
44 </help>
45 <citations>
46 <citation></citation>
47 </citations>
48 </tool>