Mercurial > repos > simon-gladman > fasta_stats

changeset 0:153f7a414921 draft

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Uploaded
author simon-gladman
date Tue, 25 Jun 2013 01:51:03 -0400
parents
children 20ca2574216a
files fasta-stats.xml
diffstat 1 files changed, 38 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta-stats.xml	Tue Jun 25 01:51:03 2013 -0400
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+<tool id="fasta-stats" name="Fasta Statistics" version="1.0.0">
+    <description>Display summary statistics for a fasta file.</description>
+    <command interpreter="perl">
+        fasta-stats.pl $dataset > $stats
+    </command>
+    <inputs>
+        <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/>
+    </inputs>
+    <outputs>
+        <data name="stats" format="tabular" label="${tool.name} on ${on_string}: Fasta summary stats"/>
+    </outputs>
+    
+    <help>
+**Fasta Stats**
+Displays the summary statistics for a fasta file.
+
+Written by Torsten Seemann - Victorian Bioinformatics Consortium
+
+Wrapped by Simon Gladman - Victorian Bioinformatics Consortium
+
+------
+
+Outputs in tabular form:
+    Lengths: n50, min, max, median and average
+    
+    Number of base pairs: A, C, G, T, N, Total and Total_not_N
+    
+    Number of sequences
+    
+    GC content in %
+
+------
+
+Inputs:
+
+Fasta dataset    
+    </help>
+</tool>