view irods_download.xml @ 0:7d8912d20007 draft

"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"

<tool id="irods_download" name="iRODS Download" version="0.1" workflow_compatible="false">
	<description>Download your files from iRODS into 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 ###
		## Set up iRODS params
		#import json
		#set params = {}
		#set params["irods_host"] = str($custom_host)
		#set params["irods_port"] = str($custom_port)
		#set params["irods_zone"] = str($custom_zone)
		##set params["filepath"] = str($file_path)

		#if $file_select_config.selection_type == "use_path"
		#set params["selection_type"] = "path"
		#set params["file_path"] = str($file_select_config.file_path)
		#set params["expl_path"] = ""
		#end if
		#if $file_select_config.selection_type == "use_explorer"
		#set params["selection_type"] = "explorer"
		#set params["file_path"] = ""
		#set params["expl_path"] = str($file_select_config.explorer_entrypoint)
		#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["galaxy_root"] = str($GALAXY_ROOT_DIR)
		#set params["galaxy_datatypes"] = str($GALAXY_DATATYPES_CONF_FILE)
		##import os
		##import glob
		##set $test = glob.glob("os.getcwd()" + "/**/irods_galaxy_registry.xml", recursive=True)
		##set params["reg_file"]
		#set params["tool_type"] = "down"
		#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:" />
		<conditional name="file_select_config">
			<param type="select" display="radio" name="selection_type" label="File Selection:">
				<option value="use_path">Use path to iRODS File or Directory</option>
				<option value="use_explorer">Use file explorer</option>
			</param>
			<when value="use_path">
				<param name="file_path" type="text" value="E.g.: /ZONE/home/USER/my_data.txt" label="Path to iRODS File or Directory:" />
			</when>
			<when value="use_explorer">
				<param name="explorer_entrypoint" type="text" value="" label="Entry directory for file explorer (optional):" />
			</when>
		</conditional>
	</inputs>

	<outputs>
		<data name="output" label="${tool.name}: " auto_format="true" />
	</outputs>

	<help>
Download iRODS

	</help>
	 <citations>
        	<citation type="bibtex">
@misc{Download-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>