Mercurial > repos > rhohensinner > galaxy_irods_interface
diff tug_upload.xml @ 2:0641ea2f75b1 draft
"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
author | rhohensinner |
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date | Fri, 02 Jul 2021 09:40:25 +0000 |
parents | |
children | d2be2eb8350f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tug_upload.xml Fri Jul 02 09:40:25 2021 +0000 @@ -0,0 +1,70 @@ +<tool id="irods_upload" name="iRODS Upload" version="0.2" 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) + 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>