# HG changeset patch
# User nml
# Date 1592922336 14400
# Node ID c9a43abcd993f4f011a98bdd9e8e4cae35bfb323
# Parent  c27b4346352f7af925c3fc80b4695fe0549f4446
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"

diff -r c27b4346352f -r c9a43abcd993 filter-density.xml
--- a/filter-density.xml	Tue Aug 27 12:30:47 2019 -0400
+++ b/filter-density.xml	Tue Jun 23 10:25:36 2020 -0400
@@ -1,8 +1,9 @@
-<tool id="filterdensity" name="Filter Density" version ="1.8.2">
+<tool id="filterdensity" name="Filter Density" version ="@VERSION@+galaxy1">
   <description>Identify high density positions within indvidual genomes</description>
-  <requirements>
-    <requirement type="package" version="1.8.2">snvphyl-tools</requirement>
-  </requirements>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <command detect_errors="exit_code">
       bcftools plugin filter_snv_density $vcf -O b -o $filtered_bcf -- --filename $vcf --region_file $out
       #if $window_size:
@@ -14,8 +15,8 @@
   </command>
   <inputs>
     <param name="vcf" type="data" label="Input vcf file" format="vcf" />
-    <param name="window_size" type="integer" label="Size of search window" format="" optional="true"/>
-    <param name="threshold"  type="integer" label="Density threshold cutoff" format="" optional="true"/>
+    <param name="window_size" type="integer" min="1" label="Size of search window" format="" optional="true"/>
+    <param name="threshold"  type="integer"  min="1" label="Density threshold cutoff" format="" optional="true"/>
   </inputs>
   <outputs>
     <data format="txt" name="out" label="High density regions"/>
@@ -45,8 +46,5 @@
   - threshold - The threshold distance between SNV's in order for them to be considered 'high density'
   - window_size - The size of the window, in base pairs, that will be looked at at any given time to calculate density.
   </help>
-
-  <citations>
-  </citations>
-
+  <expand macro="citations"/>
 </tool>
diff -r c27b4346352f -r c9a43abcd993 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Jun 23 10:25:36 2020 -0400
@@ -0,0 +1,16 @@
+<macros>
+  <token name="@VERSION@">1.8.2</token>
+
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="@VERSION@">snvphyl-tools</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+  <xml name="citations">
+    <citations>
+      <citation type="doi">10.1099/mgen.0.000116</citation>
+      <yield/> 
+    </citations>
+  </xml>
+</macros>