Mercurial > repos > rhohensinner > galaxy_irods_interface

comparison tug_download.xml @ 2:0641ea2f75b1 draft

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"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
author rhohensinner
date Fri, 02 Jul 2021 09:40:25 +0000
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children d2be2eb8350f
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1:19c1cecdfdfd 2:0641ea2f75b1
1 <tool id="irods_download" name="iRODS Download" version="0.2" workflow_compatible="false">
2 <description>Download your files from iRODS into Galaxy</description>
3 <requirements>
4 <requirement type="package" version="0.8.2">python-irodsclient</requirement>
5 </requirements>
6
7 <command interpreter="python">
8 ### using CHEETAH ###
9 ## Set up iRODS params
10 #import json
11 #set params = {}
12 #set params["irods_host"] = str($custom_host)
13 #set params["irods_port"] = str($custom_port)
14 #set params["irods_zone"] = str($custom_zone)
15 ##set params["filepath"] = str($file_path)
16 #set params["file_path"] = str($file_path)
17 ## set up Galaxy params
18 #set params["galaxy_user"] = str($__user_name__)
19 #set params["job_id"] = str($output.creating_job.id)
20 #set params["out_dir"] = str($output.files_path)
21 #set params["out_file"] = str($output)
22 #set params["galaxy_root"] = str($GALAXY_ROOT_DIR)
23 #set params["galaxy_datatypes"] = str($GALAXY_DATATYPES_CONF_FILE)
24 #set params["irods_user"] = str($user)
25 #set params["irods_password"] = str($password)
26 ##import os
27 ##import glob
28 ##set $test = glob.glob("os.getcwd()" + "/**/irods_galaxy_registry.xml", recursive=True)
29 ##set params["reg_file"]
30 #set params["tool_type"] = "down"
31 #set $params=json.dumps($params)
32 main.py '$params'
33 </command>
34
35 <inputs>
36 <param name="custom_host" type="text" value="data.cyverse.tugraz.at" label="iRODS Host:" />
37 <param name="custom_port" type="text" value="1247" label="iRODS Port:" />
38 <param name="custom_zone" type="text" value="TUG" label="iRODS Zone:" />
39 <param name="file_path" type="text" value="E.g.: /ZONE/home/USER/my_data.txt" label="Path to iRODS File or Directory:" />
40 <param name="user" type="text" value="" label="iRODS User:" />
41 <param name="password" type="text" value="" label="iRODS Password:" />
42 </inputs>
43
44 <outputs>
45 <data name="output" label="${tool.name}: ${file_path}" auto_format="true" />
46 </outputs>
47
48 <help>
49 Download iRODS
50
51 </help>
52 <citations>
53 <citation type="bibtex">
54 @misc{Download-iRODS,
55 author = {Hohensinner, Richard},
56 year = {2021},
57 title = {iRODSTools},
58 publisher = {GitLab},
59 journal = {GitLab repository},
60 url = {https://gitlab.tugraz.at/D463A320ED7901AB/galaxy_irods_tools},
61 }
62 </citation>
63 </citations>
64 </tool>