Mercurial > repos > simon-gladman > fasta_extract

changeset 1:5dfc014a8b3a draft default tip

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Uploaded
author simon-gladman
date Tue, 25 Jun 2013 01:48:56 -0400
parents bcb73a63ffee
children
files fa-extract-sequence.xml
diffstat 1 files changed, 38 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fa-extract-sequence.xml	Tue Jun 25 01:48:56 2013 -0400
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+<tool id="fa-extract-sequence" name="Fasta Extract Sequence" version="1.0.0">
+    <description>Extract a single sequence from a fasta file.</description>
+    <command interpreter="perl">
+        fa-extract-few.pl
+        -f $dataset
+        $id
+        > 
+        $output
+    </command>
+    <inputs>
+        <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/>
+        <param name="id" type="text" label="Sequence ID (or partial)" help="Name of the sequence to extract. Will also match partial names and return all matches." />
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" label="${tool.name} on ${on_string}: Fasta"/>
+    </outputs>
+    
+    <help>
+**Fasta Extract Sequence**
+Extracts a fasta sequence from a multfasta by id (exact or partial)
+
+Written by Torsten Seemann - Victorian Bioinformatics Consortium
+
+Wrapped by Simon Gladman - Victorian Bioinformatics Consortium
+
+------
+
+Outputs in fasta format.
+    
+------
+
+Inputs:
+
+Fasta dataset
+
+Sequence id
+    </help>
+</tool>