diff feature_sync.xml @ 0:c01c63c043f0 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/feature_sync.xml	Mon Sep 11 05:53:20 2017 -0400
@@ -0,0 +1,77 @@
+<?xml version="1.0"?>
+<tool id="feature_sync" profile="16.04" name="Synchronize features" 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 feature sync
+
+            #for $rep in $repeat_types:
+                --types '${rep.types}'
+            #end for
+
+            #for $rep in $repeat_ids:
+                --ids '${rep.ids}'
+            #end for
+
+            --organism_id '${organism_id}'
+
+        &&
+
+        echo "Data loaded" > $results
+    ]]></command>
+    <inputs>
+        <param argument="--organism_id"
+               type="select"
+               dynamic_options="list_organisms()"
+               label="Organism" />
+
+        <repeat name="repeat_types" title="Feature types">
+            <param name="types"
+                   argument="--types"
+                   type="text"
+                   optional="true"
+                   label="Feature type to synchronize"
+                   help="Type of records to be synced (e.g. 'gene' or 'mRNA')" />
+        </repeat>
+
+        <repeat name="repeat_ids" title="Feature ids">
+            <param name="ids"
+                   argument="--ids"
+                   type="text"
+                   optional="true"
+                   label="Feature to synchronize"
+                   help="Name of a feature to be synced (e.g. 'gene0001')" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data format="txt" name="results" label="Synchronize features into Tripal" />
+    </outputs>
+    <tests>
+        <test expect_failure="true">
+            <param name="organism" value="Testus testus" />
+            <param name="types" value="gene mRNA" />
+            <param name="types" value="gene0001 gene0002" />
+
+            <expand macro="test_result" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        @HELP_OVERVIEW@
+
+        **Synchronize Features**
+
+        With this tool, you can synchronize some features from the Chado database into the Tripal instance.
+        A corresponding Drupal node will be created for each feature.
+
+        @HELP@
+    ]]></help>
+    <expand macro="citation"/>
+</tool>