# HG changeset patch
# User estrain
# Date 1670955897 0
# Node ID 59dc279294b62382c11fb391999ca2bb2b2aa219
# Parent  6690f5040e0589be6a53b0f2b7f98bbbc1160b9a
Uploaded

diff -r 6690f5040e05 -r 59dc279294b6 lissero.xml
--- a/lissero.xml	Sun Dec 11 15:55:49 2022 +0000
+++ b/lissero.xml	Tue Dec 13 18:24:57 2022 +0000
@@ -1,51 +1,51 @@
-<tool id="lissero" name="lissero" 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.
-  --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]
-
-    ]]></help>
-    <citations>
-      <citation type="doi">10.1128/JCM.42.8.3819-3822.2004</citation> 
-    </citations>
-</tool>
+<tool id="lissero" name="lissero" 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.
+  --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]
+
+    ]]></help>
+    <citations>
+      <citation type="doi">10.1128/JCM.42.8.3819-3822.2004</citation> 
+    </citations>
+</tool>