# HG changeset patch
# User nml
# Date 1566923447 14400
# Node ID c27b4346352f7af925c3fc80b4695fe0549f4446

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

diff -r 000000000000 -r c27b4346352f filter-density.xml
--- /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>
diff -r 000000000000 -r c27b4346352f test-data/1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.vcf	Tue Aug 27 12:30:47 2019 -0400
@@ -0,0 +1,38 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
+##contig=<ID=1,length=2147483647>
+##contig=<ID=2,length=2147483647>
+##contig=<ID=3,length=2147483647>
+##contig=<ID=4,length=2147483647>
+##contig=<ID=5,length=2147483647>
+##contig=<ID=20,length=2147483647>
+##FILTER=<ID=Test,Description="Test filter">
+##INFO=<ID=DP2,Number=2,Type=Integer,Description="Depth">
+##FORMAT=<ID=DP2,Number=2,Type=Integer,Description="Depth">
+##contig=<ID=12,length=123456789>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	AAA0001	BBB0002
+2	101	.	ATTTTTTTTTTTTT	ATTTTTTTTTTTTTTT	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
+2	114	.	TC	TTCC,TTC	999	PASS	INDEL;AN=4;AC=2,2	GT:DP	1/2:1	1/2:1
+2	115	.	C	T	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
+20	3	.	G	CT	999	PASS	INDEL;AN=4;AC=2	GT	0/1	0/1
+20	3	.	GATG	GACT	999	PASS	INDEL;AN=4;AC=2	GT	1/0	1/0
+20	5	.	TGGG	TAC,TG,TGGGG,AC	.	PASS	INDEL;AN=4;AC=2,2,0,0	GT:PL:DP	1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1	1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1
+20	59	.	AG	.	999	PASS	AN=4	GT:PL:DP	0/0:0:4	0/0:0:4
+20	80	.	CACAG	CACAT	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	81	.	A	C	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	95	.	TCACCG	ACACCG	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	95	.	TCACCG	AAAAAA	999	Test	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	273	.	CAAAAAAAAAAAAAAAAAAAAA	CAAAAAAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=4;AC=2,2	GT:PL:DP	1/2:0,3,5,3,5,5:1	1/2:0,3,5,3,5,5:1
+20	274	.	AAAAAAAAA	AAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+20	278	.	AAAAAAAAAAAAAAAAA	AAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+3	10	.	GTGGAC	GTGGACACAC,GTGGACAC,GTGGACACACAC,GTGG,GTGGACACACACAC,ATGGACACACAC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+3	15	.	CACA	CAC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+4	21	.	ATTTTTTTTTTTTTTTC	ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+5	22	.	A	AGA	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
diff -r 000000000000 -r c27b4346352f test-data/bcf1.bcf
Binary file test-data/bcf1.bcf has changed
diff -r 000000000000 -r c27b4346352f test-data/density_regions.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/density_regions.txt	Tue Aug 27 12:30:47 2019 -0400
@@ -0,0 +1,5 @@
+2	101	115
+20	3	95
+20	273	278
+3	10	15
+#Calculation and writing of high density regions has completed.