Mercurial > repos > john-mccallum > dnaclust

diff cut_dnaclust.xml @ 0:84be1fe7e34a draft

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author john-mccallum
date Thu, 06 Sep 2012 23:05:22 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cut_dnaclust.xml	Thu Sep 06 23:05:22 2012 -0400
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<tool id="cutClust_1" name="cutClust">
+  <description>Remove clusters below a certain depth</description>
+  <command >cut -f $depth- $inputFile | sed '/^$/d'   | sort | uniq >  $outputfile</command>
+  <inputs>
+    <param format="tabular" name="inputFile" type="data" label="Columnar Input File" help="tabular file of DNAclust clusters" />
+ <param name="depth" size="10" type="text" value="50" label="Minimum depth for cutoff" />
+
+  </inputs>
+  <outputs>
+     <data format="tabular"  name="outputfile" />
+  </outputs>
+<help>
+.. class:: infomark
+
+**TIP**
+
+::
+
+This tool simply cuts off columns from the left
+e.g. set to 2 to remove singletons, 50 to remove clusters with less than 50 reads
+</help>
+
+
+</tool>