Mercurial > repos > artbio > cherry_pick_fasta
comparison cherry_pick_fasta.xml @ 0:e3aee4ba49c6 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
| author | artbio |
|---|---|
| date | Sun, 15 Oct 2017 13:26:45 -0400 |
| parents | |
| children | ea8fde9c6f82 |
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| -1:000000000000 | 0:e3aee4ba49c6 |
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| 1 <tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="1.0.0"> | |
| 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 $output | |
| 7 </command> | |
| 8 | |
| 9 <inputs> | |
| 10 <param name="query" type="text" size="30" value="" label="Select sequences with this string in their header" help="exemple: gi|40557596"> | |
| 11 <sanitizer> | |
| 12 <valid initial="string.printable"> | |
| 13 <remove value="""/> | |
| 14 <remove value="\"/> | |
| 15 </valid> | |
| 16 <mapping initial="none"> | |
| 17 <add source=""" target="\""/> | |
| 18 <add source="\" target="\\"/> | |
| 19 </mapping> | |
| 20 </sanitizer> | |
| 21 </param> | |
| 22 <param format="fasta" label="Source file" name="input" type="data" /> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data name="output" format="fasta" label="${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 </tool> |