# HG changeset patch
# User nml
# Date 1566923512 14400
# Node ID 7f27672ff88020c816507db4aa80f1a0f7c60a05

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

diff -r 000000000000 -r 7f27672ff880 find-repeats.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/find-repeats.xml	Tue Aug 27 12:31:52 2019 -0400
@@ -0,0 +1,46 @@
+<tool id="findrepeat" name="Find Repeats" version ="1.8.2">
+  <description>Identify repeat elements using Mummer</description>
+  <requirements>
+    <requirement type="package" version="1.8.2">snvphyl-tools</requirement>
+    <requirement type="package" version="3.23">mummer</requirement>
+  </requirements>
+  <command detect_errors="exit_code">
+      find-repeats.pl -l $length -p $pid $fasta > $out
+  </command>
+  <inputs>
+    <param name="fasta" type="data"  label="Fasta file" format="fasta"/>
+    <param name="length"  label="Minimum length of repeat region" type="integer" value="150"/>
+    <param name="pid"   label="Minimum PID of repeat region" type="integer" value="90"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="length" value="150"/>
+      <param name="pid" value="90"/>
+      <param name="fasta" value="find-repeats-input-1.fasta"/>
+      <output name="out" file="find-repeats-output-1.tabular"/>
+    </test>
+  </tests>
+
+  <help>
+What it does
+============
+
+Searches a fasta reference file for repeats.
+
+
+Usage
+=====
+
+**Parameters**
+  - Fasta file:  A fasta reference file to search for repeats.
+
+**Options**
+  - Minimum length of repeat region (150).
+  - Minimum PID of repeat region (90).
+  </help>
+<citations>
+</citations>
+</tool>
diff -r 000000000000 -r 7f27672ff880 test-data/find-repeats-input-1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find-repeats-input-1.fasta	Tue Aug 27 12:31:52 2019 -0400
@@ -0,0 +1,8 @@
+>A
+CCCGCTCGCCACGCTTTGGCCATAGTGCTGCCTTCTACGATGTGTAAACCGTGCAACTTAATGCCATCGGTGCCTACCTT
+CAGTACTTGCTGTAACGTGGTGAGGTTTTCAGTGCGCTCTTCACCGGGTAACCCAACAATCAAGTGAGTACACACTTTGA
+TACCTAACGCTCTAGCTTTGGCAGTGATCTCTGCGTAGCAGGCAAAATCGTGCCCGCGGTTAATGCGTTTTAAAGTCTGG
+>B
+CCCGCTCGCCACGCTTTGGCCATAGTGCTGCCTTCTACGATGTGTAAACCGTGCAACTTAATGCCATCGGTGCCTACCTT
+CAGTACTTGCTGTAACGTGGTGAGGTTTTCAGTGCGCTCTTCACCGGGTAACCCAACAATCAAGTGAGTACACACTTTGA
+TACCTAACGCTCTAGCTTTGGCAGTGATCTCTGCGTAGCAGGCAAAATCGTGCCCGCGGTTAATGCGTTTTAAAGTCTGG
diff -r 000000000000 -r 7f27672ff880 test-data/find-repeats-output-1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find-repeats-output-1.tabular	Tue Aug 27 12:31:52 2019 -0400
@@ -0,0 +1,4 @@
+A	1	240
+B	1	240
+B	1	240
+A	1	240