<tool id="synapse_upload" name="Synapse Upload" version="3.0.1">
	<description>Create Synapse</description>
	<requirements>
		<requirement type="package" version="0.5.1">synapseclient</requirement>
	</requirements>
	<command interpreter="python">synapse_galaxy_client.py upload $script_file 
$etype 
$properties_file 
$annotations_file 
$outfile

#if str($attachment) != ''
$attachment
#else
-
#end if

#if str($attachment_name) != ''
$attachment_name
#else
-
#end if


#if str($synid) != ''
$synid
#else
-
#end if
</command>
	<request_param_translation>
        <request_param galaxy_name="sessionToken" remote_name="sessionToken" missing="" />
    </request_param_translation>
	<inputs>
		<param name="user" type="text" size="90" label="Username">
			<sanitizer>
				<valid initial="string.printable"/>
			</sanitizer>
		</param>
		<param name="pass" type="text" size="90" label="Password" help="If you have a sessionToken, you don't have to enter your password">
			<sanitizer>
				<valid initial="string.printable"/>
			</sanitizer>
		</param>
		<param name="sessionToken" type="text" size="90" label="SessionToken" help="Log in via OpenID using the Link in the help section"/>
		<param name="name" type="text" size="90" label="Entity Name"/>
		<param name="synid" type="text" size="30" label="Synapse ID" help="Leave Blank to create new Entity"/>
		<param name="attachment" type="data" optional="true" label="Attachment"/>
		<param name="attachment_name" type="text" size="90" optional="true" label="Attachment Name"/>
		<param name="etype" type="select" label="Entity Type">
			<option value="Data">Data</option>
			<option value="Folder">Folder</option>
		</param>
		<param name="parentId" type="text" size="30" label="Parent ID"/>
		<repeat name="properties" title="Properties">
			<param name="name" type="select" size="90" label="Name">
				<option value="description">Description</option>
				<option value="species">Species</option>
				<option value="numSamples">Number of Samples</option>
				<option value="disease">Disease</option>
				<option value="tissueType">Tissue Type</option>
			</param>
			<param name="value" type="text" size="90" label="Value">
				<sanitizer>
					<valid initial="string.printable">
						<remove value="&quot;"/>
					</valid>
					<mapping initial="none">
						<add source="&quot;" target="\&quot;"/>
					</mapping>
				</sanitizer>
			</param>
		</repeat>
		
		<repeat name="annotations" title="Annotations">
			<param name="name" type="text" size="90" label="Name"/>
			<param name="value" type="text" size="90" label="Value">
				<sanitizer>
					<valid initial="string.printable">
						<remove value="&quot;"/>
					</valid>
					<mapping initial="none">
						<add source="&quot;" target="\&quot;"/>
					</mapping>
				</sanitizer>
			</param>		
		</repeat>
		
	</inputs>
	<outputs>
		<data format="txt" name="outfile" />
	</outputs>
	<configfiles>
		<configfile name="script_file">#if str($sessionToken) != ''
token
$sessionToken
#else
password
$user
$pass
#end if
</configfile>
		<configfile name="properties_file">parentId	$parentId
#for a in $properties:
${a.name}	${a.value}
#end for
#if str($name) != ''
name	$name
#end if
</configfile>
		<configfile name="annotations_file">#for a in $annotations:
${a.name}	${a.value}
#end for
</configfile>

	</configfiles>
		<help>

Login via OpenID |location_link|.

.. |location_link| raw:: html

   &lt;a href="https://synapse.sagebase.org/Portal/openid?OPEN_ID_PROVIDER=GOOGLE&amp;RETURN_TO_URL=${host_url}?tool_id=synapse_upload&amp;" target="_blank"&gt;at Synapse&lt;/a&gt;

	</help>

</tool>