diff versioned_data.xml @ 1:5c5027485f7d draft

Uploaded correct file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/versioned_data.xml	Sun Aug 09 16:07:50 2015 -0400
@@ -0,0 +1,124 @@
+<tool id="versioned_data" name="Versioned data retrieval" version="0.1.03">
+	<description>Retrieve versioned sequence files and/or their blast, bowtie, etc. database indexes</description>
+	<macros>
+		<token name="@BINARY@">versioned_data.py</token>
+		<import>bccdc_macros.xml</import>
+	</macros>
+	<expand macro="requirements" />
+	<command interpreter="python">
+		#assert $__user__, Exception( 'You must be logged in to use this tool.' )
+		versioned_data.py
+		#if $globalRetrievalDate.strip() > ''
+			-d "$globalRetrievalDate"
+		#end if
+		-r 
+		"
+		#for $v in $versions:
+			${v.database},
+			#for $r in $v.retrieval:
+				${r.retrievalId}
+			#end for
+			,
+			#for $w in $v.workflows:
+				${w.workflow}
+			#end for
+			|
+		#end for
+		"		
+		-o "$log"
+		-O "$__app__.security.encode_id($log.id)"
+		--api_info_path "$api_info_path" ##Actually a file path to configfile that holds api key
+	</command>
+	<!--  #:$log.hid:$log.id dataset_id -->
+	<expand macro="stdio" />
+	
+	<inputs>
+		<!-- Implement as datepicker? http://www.learnfaceit.org/for-developers/adding-parameter-types-to-tool -->
+		<param name="globalRetrievalDate" type="text" label="Global retrieval date [YYYY-MM-DD]" help="The recall system will use this date to try to select the appropriate versions below.  Leave empty to select current versions." size="25" />
+
+		<param name="api_info" display="radio" type="drill_down" label="For user with Galaxy API Key" dynamic_options="vdb_init_tool_user(__trans__)" />
+
+		<repeat name="versions" title="Data Source" min="1" max="15">
+
+			<param name="database" type="select" label="Data" dynamic_options="vdb_get_databases()" multiple="false" />
+
+			<repeat name="retrieval" title="Retrieval" min="0" max="1">
+				<param name="retrievalId" label="Version date/id" type="select" dynamic_options="vdb_get_versions(database, globalRetrievalDate)"/>
+			</repeat>
+			
+			<repeat name="workflows" title="Workflow" min="0" max="5" > 
+				<param name="workflow" type="select" label="Name" dynamic_options="vdb_get_workflows(database)" />
+			</repeat>
+
+		</repeat>
+				
+	</inputs>
+	
+	<configfiles>
+		<configfile name="api_info_path">${__user__.api_keys[0].key}
+			$api_info
+		</configfile>
+	</configfiles>
+
+	<outputs>
+		<data name="log" format="txt" label="Versioned Data Retrieval" />
+    </outputs>
+
+	<code file="versioned_data_form.py" />
+	
+	<tests>
+		<test>
+			<param name="db_type" value="nucl"/>
+			<!-- ... -->
+		</test>
+	</tests>
+
+    <help>
+    
+.. class:: infomark
+
+
+**What it does**
+
+This tool retrieves links to current or past versions of fasta or other types of  
+data from a cache kept in the Galaxy data library called "Versioned Data".  It then places 
+them into one's current history so that subsequent tools can work with that data.  
+
+For example, after using this tool to select a version of the NCBI nt database, a blast search can be carried out on it by selecting "BLAST database from your history" from the "Subject database/sequences" field of the NCBI BLAST+ search tool.
+
+You can select one or more files or databases by version date or id. This list 
+is supplied from the Shared Data > Data Libraries > Versioned Data folder that has
+been set up by an administrator.
+
+The Workflows section allows you to select one or more pre-defined workflows 
+to execute on the versioned data.  The results are placed in your history for use 
+by other tools or workflows.
+  
+A caching system exists to cache the versioned data or workflow data that the tool generates.  
+If you request versioned data or derivative data that isn't cached, it may take time to regenerate. 
+
+The top-level "Global retrieval date [YYYY-MM-DD]" field that the form starts with will be applied to 
+all selected databases.  This can be overriden by a retrieval date or version that 
+you supply for a particular database.  Leave it and any "Retrievals" inputs empty if you just need the latest version of selected databases.
+
+-------
+
+.. class:: warningmark
+
+**Note**
+
+Again, some past database versions can take time to regenerate if there is no cached version available, for example NCBI nt is a 50+ gigabyte file that needs to be read through to get a fasta version, and a makeblastdb workflow on top of that can take hours on the first call.  Access to cached versions is immediate.
+
+Setup of versioned data sources and workflow options can only be done by a Galaxy administrator.
+
+-------
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following paper:
+
+*Reference coming soon...*
+
+    </help>
+</tool>