# HG changeset patch
# User p.lucas
# Date 1718100325 0
# Node ID eb1a6c7786886124a57e30a3b49050d55087300c

Uploaded wrapper

diff -r 000000000000 -r eb1a6c778688 VCF_create_major_and_minor_reference_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/VCF_create_major_and_minor_reference_wrapper.xml	Tue Jun 11 10:05:25 2024 +0000
@@ -0,0 +1,37 @@
+<tool id="get_major_minor_sequence" name="Create major and minor sequence with lofreq result" version="1">
+  <description>
+    From lofreq result and the reference sequence used in alignment get
+    the MAJOR and the MINOR sequence in fasta format.
+    Provide 2 output fasta file, one sequence in each file.
+  </description>
+  <requirements>
+    <requirement type="package" version="1.79">biopython</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command interpreter="python" detect_errors="exit_code"><![CDATA[
+    VCF_create_major_and_minor_reference.py 
+      -v "$lofreq_output" 
+      -r "$reference_fasta" 
+      -M "$output_major"
+      -m "$output_minor"
+  ]]></command>
+  <inputs>
+    <param name="lofreq_output" type="data" format="vcf" label="Lofreq output" help="Lofreq output file in vcf format."/>
+    <param name="reference_fasta" type="data" format="fasta" label="Reference file" help="Reference file used with lofreq"/>
+  </inputs>
+  <outputs>
+    <data format="fasta" name="output_major" label="${tool.name} on ${on_string}: MAJOR"/>
+    <data format="fasta" name="output_minor" label="${tool.name} on ${on_string}: MINOR"/>
+  </outputs>
+  <help>
+  <![CDATA[
+
+Homemade script to create two references with lofreq output:
+  - one file with all MAJOR mutation
+  - one file with all MINOR mutation
+
+  ]]>
+  </help>
+</tool>