Mercurial > repos > rhohensinner > galaxy_irods_interface
view irods_download.xml @ 1:19c1cecdfdfd draft
"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
author | rhohensinner |
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date | Wed, 23 Jun 2021 10:40:19 +0000 |
parents | 7d8912d20007 |
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<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>