changeset 10:a06251a4625b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/updater/discard_from_collection.xml	Mon Sep 26 09:27:16 2016 -0400
@@ -0,0 +1,116 @@
+<tool id="vl_update_discard_from_collection" name="VLU.discard_from_collection">
+  <description>
+    Discard input elements from the selected collection
+  </description>
+  <command interpreter="python">
+    discard_from_collection.py
+    #if $advanced_configuration.configuration_level == 'advanced'
+      --host=$advanced_configuration.vl_host
+      --user=$advanced_configuration.vl_user
+      --passwd=$advanced_configuration.vl_passwd
+    #end if
+    --loglevel=$__app__.config.vl_loglevel
+    --logfile=${logfile}
+    --ifile=${ifile}
+    #if str($collection_selector.collection_type) != 'no_coll_selected'
+      --collection_type=${collection_selector.collection_type}
+      #if str($collection_selector.collection_type) == 'DataCollection'
+        #if str($collection_selector.dcoll_label) != 'no_label_selected'
+          --collection_label=${collection_selector.dcoll_label}
+	#end if
+      #elif str($collection_selector.collection_type) == 'VesselsCollection'
+        #if str($collection_selector.vcoll_label) != 'no_label_selected'
+          --collection_label=${collection_selector.vcoll_label}
+	#end if
+      #end if
+    #end if
+  </command>
+
+  <inputs>
+    <param format="tabular" name="ifile" type="data"
+	   label="A tabular dataset with the following columns..."/>
+
+    <conditional name="collection_selector">
+      <param name="collection_type" type="select"
+	     label="Collection Type">
+	<option value="no_coll_selected">Select a Collection type...</option>
+	<option value="DataCollection">Data Collection</option>
+	<option value="VesselsCollection">Vessels Collection</option>
+      </param>
+      <when value="DataCollection">
+	<param name="dcoll_label" type="select" label="Data Collection label"
+	       help="Choose one of the already defined Data Collections.">
+	  <options from_parameter="tool.app.known_data_collections"
+		   transform_lines="[ &quot;%s%s%s&quot;
+	                              % (l[1], self.separator, l[1])
+				      for l in obj ]">
+	    <column name="value" index="1"/>
+	    <column name="name" index="0"/>
+	    <filter type="sort_by" column="0"/>
+	    <filter type="add_value" name="Select a Data Collection..."
+		    value="no_label_selected" index="0"/>
+	  </options>
+	</param>
+      </when>
+      <when value="VesselsCollection">
+	<param name="vcoll_label" type="select" label="Vessels Collection label"
+	       help="Choose one of the already defined Vessels Collections.">
+	  <options from_parameter="tool.app.known_vessels_collections"
+		   transform_lines="[ &quot;%s%s%s&quot;
+	                              % (l[1], self.separator, l[1])
+				      for l in obj ]">
+	    <column name="value" index="1"/>
+	    <column name="name" index="0"/>
+	    <filter type="sort_by" column="0"/>
+	    <filter type="add_value" name="Select a Vessels Collection..."
+		    value="no_label_selected" index="0"/>
+	  </options>
+	</param>
+      </when>
+    </conditional>
+
+    <!-- ************************************************** -->
+    <conditional name="advanced_configuration">
+      <param name="configuration_level" type="select" 
+	     label="Configuration level">
+	<option value="default" selected="true">Default configuration</option>	
+	<option value="advanced">Advanced configuration</option>
+      </param>
+      <when value="default"/>
+      <when value="advanced">
+	<param name="vl_host" size="40" type="text" value="biobank05.crs4.it" 
+	       label="Omero/VL host"/>
+	<param name="vl_user" size="20" type="text" value="galaxy" 
+	       label="Omero/VL user"/>
+	<param name="vl_passwd" size="20" type="text" value="What?Me worry?" 
+	       label="Omero/VL passwd"/>
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data format="txt" name="logfile" label="${tool.name}.logfile"/>
+  </outputs>
+
+  <help>
+This tool discard from a DataCollection or a VesselCollection one or
+more items.
+
+The expected input file must be like
+
++---------------+
+|collection_item|
++---------------+
+|V013AFF22311   |
++---------------+
+|V0ABB3451516   |
++---------------+
+|V012441AAEEC   |
++---------------+
+
+Input file rows must be VIDs obtained using the **map_vid** tool.
+
+Collection must be selected using the specific selection lists that
+show only the ones imported into the system.
+  </help>
+</tool>
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