diff gmql_rest_datasets_download.xml @ 0:35d52820e7c7 draft default tip

planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gmql_rest_datasets_download.xml	Tue Jun 26 09:01:39 2018 -0400
@@ -0,0 +1,90 @@
+<tool id="gmql_download" name="GMLQ Import Dataset" version="0.1.1">
+  <macros>
+    <import>gmql_rest_macros.xml</import>
+  </macros>
+    <command><![CDATA[
+        #if $operation == 'import' :
+         python $__tool_directory__/gmql_rest_datasets.py '' -user=$authToken -cmd=import -dataset=${dataset}
+        #else :
+         python $__tool_directory__/gmql_rest_datasets.py $ds_archive -user=$authToken -cmd=download -dataset=${dataset}
+        #end if
+	  ]]></command>
+    <code file="dynamic_utils.py">
+        <hook validate_input="validate" />
+    </code>
+    <inputs>
+        <param format="gmql_user" name="authToken" type="data" label="Select user" />
+        <param name="gmql_datasets" type="data" format="gmql_repository" label="Working Datasets"/>
+        <param name="dataset" type="select" label="Select Dataset">
+            <options from_dataset="gmql_datasets">
+                <column name="value" index="0"/>
+                <filter column="1" type="static_value" value="public" keep="false"/>
+            </options>
+        </param>
+        <param name="operation" type="select" display="radio" multiple="false" label="Select the desired action">
+            <option value="import">Import data as a collection</option>
+            <option value="zip">Download zip archive</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="zip" name="ds_archive" label="${dataset} Compressed Archive">
+            <filter>operation == 'zip'</filter>
+        </data>
+        <collection name="query_results_m" type="list" label="${dataset} metadata">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;[\w]+)\.(?P&lt;ext&gt;[^\._]+)?"
+                               directory="metadata"/>
+            <filter>operation == 'import'</filter>
+        </collection>
+        <collection name="query_results_s" type="list" label="${dataset}">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;[\w]+)\.(?P&lt;ext&gt;[^\._]+)?"
+                               directory="samples"/>
+            <filter>operation == 'import'</filter>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="authToken" value="guest.gmql_user" />
+            <param name="gmql_datasets" value="rep.gmql_repository" />
+            <param name="dataset" value="Example1" />
+            <param name="operation" value="zip" />
+            <output name="ds_archive" file="Example1_Archive.zip" compare="sim_size" delta="0"/>
+        </test>
+        <test>
+            <param name="authToken" value="guest.gmql_user" />
+            <param name="gmql_datasets" value="rep.gmql_repository" />
+            <param name="dataset" value="Example1" />
+            <param name="operation" value="import" />
+            <collection name="query_results_s" type="list">
+               <metadata name="name" value="Example1" />
+               <discovered_dataset designation="sample1" file="sample1.bed"/>
+               <discovered_dataset designation="sample2" file="sample2.bed"/>
+               <discovered_dataset designation="sample3" file="sample3.bed"/>
+            </collection>
+            <collection name="query_results_m" type="list">
+               <metadata name="name" value="Example1 metadata" />
+               <discovered_dataset designation="sample1" file="sample1.bed.meta"/>
+               <discovered_dataset designation="sample2" file="sample2.bed.meta"/>
+               <discovered_dataset designation="sample3" file="sample3.bed.meta"/>
+            </collection>
+        </test>
+    </tests>
+    <help>
+It allows importing in the current Galaxy history the selected dataset.
+
+----
+
+**What it does**
+
+- **Import as Collection**: returning data consist of two collections, one for samples and one for their metadata
+- **Download ZIP Archive**: returns the dataset as a zip archive
+
+
+The user provides a list of datasets (gmql_repository file) and selects from there the dataset he wants to import.
+
+.. class:: warningmark
+
+A gmql_user authentication token is required for every action.
+
+  </help>
+  <expand macro="citations" />
+</tool>