# HG changeset patch
# User sanbi-uwc
# Date 1481806055 18000
# Node ID bab35d33b28deeb18a1c7fd3643c56940420b497
# Parent  bfe39c503a40db14920033db1f93e65b56ca276c
planemo upload for repository https://github.com/zipho/novo_align commit ebb00336f514938c158dfca09a48ff3c5392d806-dirty

diff -r bfe39c503a40 -r bab35d33b28d novo_align.xml
--- a/novo_align.xml	Tue Nov 29 09:18:10 2016 -0500
+++ b/novo_align.xml	Thu Dec 15 07:47:35 2016 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8" ?>
-<tool id="novo_align" name="NOVO ALIGN" version="0.0.1">
+<tool id="novo_align" name="NOVO ALIGN" version="0.0.2">
     <description>Tool to run the Novo Align mapping tool</description>
     <requirements>
         <requirement type="package" version="1.2">samtools</requirement>
@@ -65,7 +65,7 @@
     ]]></command>
     <inputs>
     <conditional name="paired_end">
-    <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" />
+    <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="yes" />
     <when value="no">
       <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" />
     </when>
@@ -102,11 +102,18 @@
         <data format="bam" name="out_file" />
     </outputs>
     <help>Help!</help>
-    <citations>
-        <citation></citation>
-    </citations>
     <tests>
         <test>
         </test>
     </tests>
+    <citations>
+        <citation type="bibtex">
+@ARTICLE{hercus2012novoalign,
+  title={Novoalign},
+  author={Hercus, C},
+  journal={Selangor: Novocraft Technologies},
+  year={2012}
+}
+        </citation>
+    </citations>
 </tool>
diff -r bfe39c503a40 -r bab35d33b28d tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Nov 29 09:18:10 2016 -0500
+++ b/tool_dependencies.xml	Thu Dec 15 07:47:35 2016 -0500
@@ -3,4 +3,7 @@
     <package name="novocraft" version="3.04.01">
         <repository changeset_revision="f3d1a01754b6" name="package_novocraft_3_04_01" owner="sanbi-uwc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
 </tool_dependency>