Mercurial > repos > rhohensinner > galaxy_irods_interface
view tug_upload.xml @ 4:84f685c067ad draft default tip
"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
author | rhohensinner |
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date | Wed, 04 Aug 2021 12:01:55 +0000 |
parents | d2be2eb8350f |
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<tool id="irods_upload" name="iRODS Upload" version="0.4" workflow_compatible="false"> <description>Upload your files to iRODS from Galaxy</description> <requirements> <requirement type="package" version="0.8.2">python-irodsclient</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($GALAXY_DATATYPES_CONF_FILE) #set params["tool_type"] = "up" #set params["irods_user"] = str($user) #set params["irods_password"] = str($password) #set $params=json.dumps($params) irods_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" /> <param name="user" type="text" value="" label="iRODS User:" /> <param name="password" type="text" value="" label="iRODS Password:" /> </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>