# HG changeset patch
# User estrain
# Date 1668894082 0
# Node ID feabac89dad3f0353605cc87df7ac6b6d43a38a9
# Parent  b09702e00f470a6c47e0a7dcd92a07754d77dfa6
Uploaded

diff -r b09702e00f47 -r feabac89dad3 lissero.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lissero.xml	Sat Nov 19 21:41:22 2022 +0000
@@ -0,0 +1,67 @@
+<tool id="lissero" name="Serogrouping typing prediction for Listeria monocytogenes" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+    <requirements>
+        <requirement type="package">lissero</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        lissero 
+        #if $advanced
+          --min_id $advanced.min_id
+          --min_cov $advanced.min_cov
+        #end_if_
+        '$input1' > '$output1'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="fasta" />
+        <conditional name="settings">
+            <param name="advanced" type="select" label="Specify advanced parameters">
+                <option value="simple" selected="true">No, use program defaults.</option>
+                <option value="advanced">Yes, see full parameter list.</option>
+            </param>
+            <when value="simple">
+            </when>
+            <when value="advanced">
+                <param name="min_id" type="float" label="Minimum percent identity to accept a match" value="95.0" min="0" max="100" /> 
+                <param name="min_cov" type="float" label="Minimum coverage of a gene to accept a match" value="95.0" min="0" max="100" /> 
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output1" format="txt" />
+    </outputs>
+    <help><![CDATA[
+        Usage: lissero [OPTIONS] FASTA...
+
+  In silico serogroup prediction for L. monocytogenes. Alleles: lmo1118,
+  lmo0737, ORF2819, ORF2110, Prs
+
+  References:
+
+  * Doumith et al. Differentiation of the major Listeria monocytogenes
+  serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22
+
+Options:
+  -h, --help              Show this message and exit.
+  -s, --serotype_db TEXT  [default:
+                          /home/strain_remote/miniconda3/lib/python3.9/site-
+                          packages/lissero/db]
+  --min_id FLOAT          Minimum percent identity to accept a match. [0-100]
+                          [default: 95.0]
+  --min_cov FLOAT         Minimum coverage of the gene to accept a match.
+                          [0-100]  [default: 95.0]
+  --debug
+  --logfile TEXT          Save log to a file instead of printing to stderr
+  --version               Show Version Information
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githublissero,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {lissero},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/MDU-PHL/lissero},
+}</citation>
+    </citations>
+</tool>