diff seqtk_sample.xml @ 2:42a473d89b08 draft

Uploaded
author iuc
date Tue, 28 Apr 2015 22:56:42 -0400
parents 33ded39275c3
children 55e75a28fde7
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_sample.xml	Tue Apr 28 22:56:42 2015 -0400
@@ -0,0 +1,38 @@
+<?xml version="1.0"?>
+<tool id="seqtk_sample" name="seqtk_sample" version="@WRAPPER_VERSION@.0">
+    <description>random subsample of fasta or fastq sequences</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[seqtk sample -s $s
+      $in_file
+      $subsample_size
+> $default]]></command>
+  <inputs>
+    <expand macro="in_faq" />
+    <param label="RNG seed" help="(-s)" name="s" type="integer" value="4"/>
+    <param label="Subsample (decimal fraction or number)" name="subsample_size" type="integer" value="100"/>
+  </inputs>
+  <outputs>
+    <data format_source="in_file" hidden="false" name="default" label="Subsample of reads from $in_file.name"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="in_file" value="seqtk_sample.fa"/>
+      <param name="subsample_size" value="4"/>
+      <param name="s" value="4"/>
+      <output name="default" file="seqtk_sample.out" ftype="fasta"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Takes a random subsample of fasta or fastq sequences. The RNG is seedable to allow for reproducible results, and defaults to `4 <http://xkcd.com/221/>`__.
+
+The subsample size can be a decimal fraction <=1, where 1 implies 100% of the reads should be used. If a number >1 is provided, that many reads will be taken from the dataset.
+
+@ATTRIBUTION@
+]]></help>
+</tool>