Mercurial > repos > gga > tripal_organism_sync

diff organism_sync.xml @ 0:98e917aa6819 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:54:11 -0400
parents
children 5d45a37e5e9b
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/organism_sync.xml	Mon Sep 11 05:54:11 2017 -0400
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+<?xml version="1.0"?>
+<tool id="organism_sync" profile="16.04" name="Synchronize an organism" version="@WRAPPER_VERSION@.0">
+    <description>from Chado to Tripal</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <code file="tripal.py"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+
+        @AUTH@
+
+        tripaille organism sync
+
+            --organism_id '${organism_id}'
+
+        &&
+
+        echo "Data loaded" > $results
+    ]]></command>
+    <inputs>
+        <param argument="--organism_id"
+               type="select"
+               dynamic_options="list_organisms()"
+               label="Organism" />
+    </inputs>
+    <outputs>
+        <data format="txt" name="results" label="Synchronize Organism into Tripal" />
+    </outputs>
+    <tests>
+        <test expect_failure="true">
+            <param name="organism_id" value="Testus testus" />
+
+            <expand macro="test_result" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        @HELP_OVERVIEW@
+
+        **Synchronize Organism**
+
+        With this tool, you can synchronize an organism from the Chado database into the Tripal instance.
+        A corresponding Drupal node will be created.
+
+        @HELP@
+    ]]></help>
+    <expand macro="citation"/>
+</tool>