diff mlst_list.xml @ 0:735872ff8222 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
author iuc
date Mon, 12 Dec 2016 15:07:38 -0500
parents
children 8e8dc9a1e3e5
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mlst_list.xml	Mon Dec 12 15:07:38 2016 -0500
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+<tool id="mlst_list" name="MLST List" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="2.6">mlst</requirement>
+    </requirements>
+
+    <version_command>mlst --version</version_command>
+
+    <command detect_errors="exit_code"><![CDATA[
+        mlst $list_type > "$report"
+    ]]></command>
+
+    <inputs>
+        <param name="list_type" type="boolean" label="Output allele information" truevalue="--longlist" falsevalue="--list"
+            help="Selecting 'Yes' will provide the alleles for all MLST schemes" optional="false" />
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="report" label="${tool.name} - list of schemes"/>
+    </outputs>
+
+    <tests>
+        <!-- Test the longlist option -->
+        <test>
+            <param name="list_type" value="true" />
+            <output name="report" ftype="txt" file="output_longlist.txt" />
+        </test>
+
+        <!-- Test the list option -->
+        <test>
+            <param name="list_type" value="false" />
+            <output name="report" ftype="txt" file="output_list.txt" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+MLST List will list all the scheme names used by MLST. Selecting the long list option will also provide the alleles for all MLST schemes.
+
+    ]]></help>
+
+    <citations>
+      <citation type="bibtex">
+        @UNPUBLISHED{Seemann2016,
+        author = "Seemann T",
+        title = "ABRicate: mass screening of contigs for antiobiotic resistance genes",
+        year = "2016",
+        note = "https://github.com/tseemann/abricate"}
+      </citation>
+    </citations>
+</tool>