# HG changeset patch
# User nicksto <nmapsy@gmail.com>
# Date 1449677631 18000
# Node ID 2aa561f29da4ff609a2d4ba315e89b00b348fb10
# Parent  e5d39283fe4d7b2c2c2817dde21d5df0bb2991b7
allele-counts.xml: Pull in new changes.

diff -r e5d39283fe4d -r 2aa561f29da4 allele-counts.xml
--- a/allele-counts.xml	Wed Dec 09 11:03:33 2015 -0500
+++ b/allele-counts.xml	Wed Dec 09 11:13:51 2015 -0500
@@ -1,13 +1,14 @@
 <tool id="allele_counts_1" version="1.2" name="Variant Annotator">
   <description> process variant counts</description>
-  <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt</command>
+  <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt -r $seed</command>
   <inputs>
     <param name="input" type="data" format="vcf" label="Input variants from Naive Variants Detector"/>
-    <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold (in percent)"/>
-    <param name="covg" type="integer" value="10" min="0" label="Coverage threshold (in reads per strand)"/>
+    <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold" help="in percent"/>
+    <param name="covg" type="integer" value="10" min="0" label="Coverage threshold" help="in reads (per strand)"/>
     <param name="nofilt" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Do not filter sites or alleles" />
     <param name="stranded" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output stranded base counts" />
     <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="True" label="Write header line" />
+    <param name="seed" type="text" value="" label="PRNG seed" />
   </inputs>
   <outputs>
     <data name="output" format="tabular"/>
@@ -17,6 +18,16 @@
     <exit_code range=":-1" err_level="fatal"/>
   </stdio>
 
+  <tests>
+    <test>
+      <param name="input" value="tests/artificial.vcf.in" />
+      <param name="freq" value="10" />
+      <param name="covg" value="10" />
+      <param name="seed" value="1" />
+      <output name="output" file="tests/artificial.csv.out" />
+    </test>
+  </tests>
+
   <help>
 
 .. class:: infomark