diff organism_add_organism.xml @ 0:51ac1ffb4f38 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
author gga
date Thu, 21 Jun 2018 08:44:11 -0400
parents
children 5d566012d85f
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/organism_add_organism.xml	Thu Jun 21 08:44:11 2018 -0400
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+<?xml version="1.0"?>
+<tool id="organism_add_organism" name="Chado organism add" version="@WRAPPER_VERSION@.0">
+ <description></description>
+	<macros>
+		<import>macros.xml</import>
+	</macros>
+	<expand macro="requirements"/>
+	<command detect_errors="aggressive"><![CDATA[
+@AUTH@
+
+chakin organism add_organism
+'$genus'
+'$common'
+'$abbr'
+
+#if $species:
+  --species '$species'
+#end if
+#if $comment:
+  --comment '$comment'
+#end if
+
+| jq -S . > $results
+    ]]></command>
+	<inputs>
+    <!-- arguments -->
+	<param name="genus" label="Genus" argument="genus" type="text" help="The genus of the organism" />
+	<param name="species" label="Species" argument="species" type="text" help="The species of the organism" />
+	<param name="common" label="Common" argument="common" type="text" help="The common name of the organism" />
+	<param name="abbr" label="Abbr" argument="abbr" type="text" help="The abbreviation of the organism" />
+
+    <!-- options -->
+	<param name="comment" label="Comment" argument="comment" type="text" help="A comment / description" />
+
+	</inputs>
+	<outputs>
+		<data format="json" name="results"/>
+	</outputs>
+	<help>
+Add a new organism to the Chado database
+
+@HELP@
+	</help>
+</tool>