# HG changeset patch
# User nml
# Date 1566923580 14400
# Node ID 317ba2ee501d8c5d200f11c529db2dcce67e2d14

"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"

diff -r 000000000000 -r 317ba2ee501d snv_matrix.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snv_matrix.xml	Tue Aug 27 12:33:00 2019 -0400
@@ -0,0 +1,39 @@
+<tool id="snvmatrix" name="SNV Matrix" version ="1.8.2">
+  <description>Create SNV matrix from Phylip file</description>
+  <requirements>
+    <requirement type="package" version="1.8.2">snvphyl-tools</requirement>
+  </requirements>
+  <command detect_errors="exit_code">
+	snv_matrix.pl   $phylip
+	-o $out
+  </command>
+  <inputs>
+    <param name="phylip" type="data" label="Phylip file" format="phylip"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="phylip" value="snvalign-13.phy"/>
+      <output name="out" file="snvalign-13.phy.out"/>
+    </test>
+  </tests>
+
+  <help>
+What it does
+============
+
+Create SNV matrix from Phylip file format
+
+
+Usage
+=====
+
+**Parameters**
+  - Phylip file: Phylogenetic file (.ph, .phy)
+
+  </help>
+<citations>
+</citations>
+</tool>
diff -r 000000000000 -r 317ba2ee501d test-data/snvalign-13.phy
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snvalign-13.phy	Tue Aug 27 12:33:00 2019 -0400
@@ -0,0 +1,6 @@
+ 5 3
+'a'	AAY
+'b'	AAA
+'c'	AAA
+'d'	TAA
+'e'	NGG
diff -r 000000000000 -r 317ba2ee501d test-data/snvalign-13.phy.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snvalign-13.phy.out	Tue Aug 27 12:33:00 2019 -0400
@@ -0,0 +1,6 @@
+strain	a	e	b	c	d	
+a	0	1	0	0	0	
+e	1	0	1	1	1	
+b	0	1	0	0	0	
+c	0	1	0	0	0	
+d	0	1	0	0	0