diff seqtk_cutN.xml @ 0:e0a0fd938de4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_cutN.xml	Thu Feb 05 11:52:40 2015 -0500
@@ -0,0 +1,52 @@
+<?xml version="1.0"?>
+<tool id="seqtk_cutN" name="seqtk_cutN" version="@WRAPPER_VERSION@.0">
+  <description>cut sequence at long N</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[seqtk cutN -n $n
+-p $p
+$g
+$in_file
+> $default]]></command>
+  <inputs>
+    <expand macro="in_faq"/>
+    <param label="min size of N tract" help="(-n)" name="n" type="integer" value="1000"/>
+    <param label="penalty for a non-N" help="(-p)" name="p" type="integer" value="10"/>
+    <param checked="false" label="print gaps only, no sequence" help="(-g)" name="g" type="boolean" falsevalue="" truevalue="-g"/>
+  </inputs>
+  <outputs>
+    <data format_source="in_file" hidden="false" name="default" label="$in_file.name split on N runs longer than $n"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="in_file" value="seqtk_cutn.fa"/>
+      <param name="n" value="1"/>
+      <output name="default" file="seqtk_cutn.out" ftype="fasta"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Splits long sequences with runs of Ns
+
+::
+
+    >test
+    AACTGATCGATCGATCGNNNNNNNNNNNACATG
+
+This will be split into the component sequences without the ambiguity.
+
+::
+
+    >test:1-17
+    AACTGATCGATCGATCG
+    >test:29-33
+    ACATG
+
+
+@ATTRIBUTION@
+      ]]></help>
+</tool>