Mercurial > repos > artbio > cherry_pick_fasta
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cherry_pick_fasta.xml Sun Oct 15 13:26:45 2017 -0400 @@ -0,0 +1,45 @@ +<tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="1.0.0"> + <description>with header satisfying a query string</description> + <command interpreter="python">cherry_pick_fasta.py + --input $input + --query-string "$query" + --output $output + </command> + + <inputs> + <param name="query" type="text" size="30" value="" label="Select sequences with this string in their header" help="exemple: gi|40557596"> + <sanitizer> + <valid initial="string.printable"> + <remove value="""/> + <remove value="\"/> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + <add source="\" target="\\"/> + </mapping> + </sanitizer> + </param> + <param format="fasta" label="Source file" name="input" type="data" /> + </inputs> + <outputs> + <data name="output" format="fasta" label="${tool.name} on ${on_string} including '${query.value}' in header" /> + </outputs> + <tests> + <test> + <param ftype="fasta" name="input" value="input.fa" /> + <param name="query" value="gi|81971654" /> + <output name="output" ftype="fasta" file="output.fa" /> + </test> + </tests> + <help> +**What it does** + +This tool retrieves nucleotide/peptide sequences from a fasta file whose headers match a given query string. + +It is Copyright © 2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_. + +.. _CNRS and University Pierre et Marie Curie: http://www.upmc.fr/en/index.html +.. _MIT license: http://opensource.org/licenses/MIT + + </help> +</tool>