diff filter-density.xml @ 0:c27b4346352f draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter-density.xml	Tue Aug 27 12:30:47 2019 -0400
@@ -0,0 +1,52 @@
+<tool id="filterdensity" name="Filter Density" version ="1.8.2">
+  <description>Identify high density positions within indvidual genomes</description>
+  <requirements>
+    <requirement type="package" version="1.8.2">snvphyl-tools</requirement>
+  </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:
+      --window_size $window_size
+      #end if
+      #if $threshold:
+      --threshold $threshold
+      #end if
+  </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"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="out" label="High density regions"/>
+    <data format="bcf" name="filtered_bcf"/>
+  </outputs>
+  <tests>
+    <test>
+    <param name="threshold" value="2"/>
+    <param name="window_size" value="100"/>
+    <param name="vcf" value="1.vcf"/>
+    <output name="out" file="density_regions.txt"/>
+    </test>
+  </tests>
+
+  <help>
+What it does
+============
+
+This script will indentify all high density SNV regions in an isolate genome, marking them as filtered-density in the associated bcf, if desired.
+
+
+Usage
+=====
+
+**Parameters**
+  - vcf - A vcf file to be analyzed for SNV density.
+  - 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>
+
+</tool>