Mercurial > repos > drosofff > cherry_pick_fasta
diff cherry_pick_fasta.xml @ 0:c7a0ec8263b4 draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
|---|---|
| date | Sun, 21 Jun 2015 14:30:50 -0400 |
| parents | |
| children | f7684171dab3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cherry_pick_fasta.xml Sun Jun 21 14:30:50 2015 -0400 @@ -0,0 +1,48 @@ +<tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="0.9.0"> + <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> + <citations> + <citation></citation> + </citations> +</tool>