Mercurial > repos > xuebing > reverse_complement

changeset 0:c7659d44142a

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Uploaded
author xuebing
date Sat, 31 Mar 2012 21:44:20 -0400
parents
children 3af9a3c6aa6f
files revcompl.xml
diffstat 1 files changed, 41 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/revcompl.xml	Sat Mar 31 21:44:20 2012 -0400
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+<tool id="revcompl" name="reverse complement">
+  <description>of DNA/RNA sequences</description>
+  <command interpreter="python">revcompl.py $input $output $fasta $rna </command>
+  <inputs>
+    <param name="input" format="txt" type="data" label="Original sequence file"/>
+    <param name="fasta" label="Check if input is fasta format" type="boolean" truevalue="fasta" falsevalue="txt" checked="False"/>
+    <param name="rna" label="Check if need to output as RNA sequences" type="boolean" truevalue="rna" falsevalue="dna" checked="False"/>
+  </inputs>
+  <outputs>
+    <data format="input" name="output" />
+  </outputs>
+  <help>
+
+**What it does**
+
+This tool outputs reverse complementary of DNA/RNA sequences in the input file. The input can be fasta format or raw sequences (each line is a sequence).
+
+Degenerate nucleotides are supported. Here is the match table:
+
+A to T/U
+
+C to G
+
+G to C
+
+T/U to A
+
+M to K
+
+W to W
+
+S to S
+
+R to Y
+
+Y to R
+
+N to N
+
+  </help>
+</tool>