# HG changeset patch
# User cropgeeks
# Date 1519056405 18000
# Node ID e24a0e2605adbf708d26ac0d8a172f92d54a4cf3

Uploaded

diff -r 000000000000 -r e24a0e2605ad germinate_importer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/germinate_importer.xml	Mon Feb 19 11:06:45 2018 -0500
@@ -0,0 +1,54 @@
+<?xml version="1.0"?>
+<!--
+    If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
+    the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
+    initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
+-->
+<tool name="Germinate 3" id="germinate_importer" tool_type="data_source" version="1.0.0">
+    <description>import data from a Germinate 3 instance</description>
+	<!--<command><![CDATA[
+  cat $output
+  ]]></command>-->
+  
+    <command><![CDATA[
+        java -jar $__tool_directory__/germinate-lib/germinate-galaxy.jar $map $genotypes
+    ]]>
+    </command>
+		
+    <!--<inputs action="http://bioinf.hutton.ac.uk/galaxy/test.html" check_values="false" method="get" target="galaxy_main">-->
+	<!--<inputs action="http://143.234.98.86:8080/germinate-demo-dev/" check_values="false" method="get" target="galaxy_main">-->
+	<inputs action="https://ics.hutton.ac.uk/resources/galaxy-germinate" check_values="false" method="get">
+        <display>Download from Germinate</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
+        <param name="tool_id" type="hidden" value="germinate_importer" />
+        <!--<param name="wibble" type="hidden" value="1" />
+        <param name="wobble" type="hidden" value="2" />
+        <param name="flump" type="hidden" value="3" />-->
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
+        <request_param galaxy_name="URL" remote_name="extraction" missing="" />
+        <!--<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" >-->
+            <!--<value_translation>
+                <value galaxy_value="auto" remote_value="primaryTable" />
+                <value galaxy_value="auto" remote_value="selectedFields" />
+                <value galaxy_value="wig" remote_value="wigData" />
+                <value galaxy_value="interval" remote_value="tab" />
+                <value galaxy_value="html" remote_value="hyperlinks" />
+                <value galaxy_value="fasta" remote_value="sequence" />
+                <value galaxy_value="gtf" remote_value="gff" />
+            </value_translation>
+        </request_param>-->
+    </request_param_translation>
+    <uihints minwidth="800"/>
+    <outputs>
+        <!--<data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/>-->
+		<data name="map" format="fjmap" label="${tool.name}"/>
+		<data name="genotypes" format="fjgenotype" label="${tool.name}"/>
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+    <citations>
+        <citation type="doi">10.1093/database/bar011</citation>
+        <citation type="doi">10.1101/gr.229102</citation>
+    </citations>
+</tool>