diff irods_upload.xml @ 0:7d8912d20007 draft

"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/irods_upload.xml	Fri May 21 09:51:30 2021 +0000
@@ -0,0 +1,66 @@
+<tool id="irods_upload" name="iRODS Upload" version="0.1" workflow_compatible="false">
+	<description>Upload your files to iRODS from Galaxy</description>
+	<requirements>
+		<requirement type="package" version="0.8.2">python-irodsclient</requirement>
+		<requirement type="package" version="0.1.0">tk</requirement>
+	</requirements>
+
+	<command interpreter="python">
+		## using CHEETAH
+		#import json
+		#set params = {}
+		#set params["irods_host"] = str($custom_host)
+		#set params["irods_port"] = str($custom_port)
+		#set params["irods_zone"] = str($custom_zone)
+		##if $irods_config.typeiRODS == "use_any_irods"
+		##set params["irods_host"] = str($irods_config.custom_host)
+		##set params["irods_port"] = str($irods_config.custom_port)
+		##set params["irods_zone"] = str($irods_config.custom_zone)
+		##end if
+		##if $irods_config.typeiRODS == "use_tug_irods"
+		##set params["irods_host"] = "data.cyverse.tugraz.at"
+		##set params["irods_port"] = "1247"
+		##set params["irods_zone"] = "TUG"
+		##end if
+		## set up Galaxy params
+		#set params["galaxy_user"] = str($__user_name__)
+		#set params["job_id"] = str($output.creating_job.id)
+		#set params["out_dir"] = str($output.files_path)
+		#set params["out_file"] = str($output)
+		#set params["up_file"] = str($up_file.name)
+		#set params["up_file_path"] = str($up_file)
+		#set params["galaxy_root"] = str($GALAXY_ROOT_DIR)
+		#set params["galaxy_datatypes"] = str($GALAXY_DATATYPES_CONF_FILE)
+		#set params["tool_type"] = "up"
+		#set $params=json.dumps($params)
+		main.py '$params'
+	</command>
+
+	<inputs>
+		<param name="custom_host" type="text" value="data.cyverse.tugraz.at" label="iRODS Host:" />
+		<param name="custom_port" type="text" value="1247" label="iRODS Port:" />
+		<param name="custom_zone" type="text" value="TUG" label="iRODS Zone:" />
+		<param name="up_file" type="data" value="" label="Galaxy file to upload" />
+	</inputs>
+
+	<outputs>
+		<data name="output" auto_format="true" />
+	</outputs>
+
+	<help>
+Upload RODS
+
+	</help>
+	 <citations>
+        	<citation type="bibtex">
+@misc{Upload-iRODS,
+  author = {Hohensinner, Richard},
+  year = {2021},
+  title = {iRODSTools},
+  publisher = {GitLab},
+  journal = {GitLab repository},
+  url = {https://gitlab.tugraz.at/D463A320ED7901AB/galaxy_irods_tools},
+}
+		</citation>
+    	</citations>
+</tool>