# HG changeset patch
# User nml
# Date 1566923468 14400
# Node ID 89c3ba37711cfcf1731392952961b54930fcb643

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

diff -r 000000000000 -r 89c3ba37711c filter-stats.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter-stats.xml	Tue Aug 27 12:31:08 2019 -0400
@@ -0,0 +1,48 @@
+<tool id="filterstat" name="Filter Stats" version ="1.8.2">
+  <description>Identify number of positions excluded based on filtered status</description>
+  <requirements>
+    <requirement type="package" version="1.8.2">snvphyl-tools</requirement>
+  </requirements>
+  <command detect_errors="exit_code">
+      filter-stats.pl -i $tabfile
+      #if $summary:
+        -a
+      #end if
+	> $out
+  </command>
+  <inputs>
+    <param name="tabfile" type="data"  label="SNV-alignment positions tab delimited file" format="tabular"/>
+    <param name="summary" type="select" display="checkboxes" label="Summary Options" multiple="true">
+        <option value="invalids">Include all entries marked as 'filtered-invalid'</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="tabfile" value="filter-stats-in.tsv" />
+      <output name="out" file="filter-stats-out.tabular" />
+    </test>
+  </tests>
+
+  <help>
+What it does
+============
+
+This script prints a stat summary of the number of N's and -'s found in the SNV-alignment positions tab delimited file.
+
+
+Usage
+=====
+
+**Parameters**
+  - input - The SNV-alignment positions tab delimited file
+
+
+**Options**
+  - -all When this option is set, the summary will include all the entries marked as 'filtered-invalid'
+  </help>
+<citations>
+</citations>
+</tool>
diff -r 000000000000 -r 89c3ba37711c test-data/filter-stats-in.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter-stats-in.tsv	Tue Aug 27 12:31:08 2019 -0400
@@ -0,0 +1,3 @@
+#Chromosome	Position	Status	Reference	query	B
+chr	5	valid	A	T	A
+chr	10	filtered-coverage	A	G	-
diff -r 000000000000 -r 89c3ba37711c test-data/filter-stats-out.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter-stats-out.tabular	Tue Aug 27 12:31:08 2019 -0400
@@ -0,0 +1,15 @@
+Chromosome	Genomes
+chr	ALL	B	query
+Total number of N's and -'s	1	1	0
+Total percent of N's and -'s	50.00	50.00	0.00
+Total number of unfiltered variants in chromosome: 2
+
+================= Filter Summary Statistics =====================
+Number of sites used to generate phylogeny: 1
+Total number of sites identified: 2
+Number of sites filtered: 1
+Percentage of sites filtered: 50.00
+Coverage filtered: 1
+mpileup filtered: 0
+Invalid filtered: Invalid positions not analyzed.  Please use -a flag to analyze.
+