Mercurial > repos > rhohensinner > galaxy_irods_interface

annotate tug_download.xml @ 4:84f685c067ad draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
author rhohensinner
date Wed, 04 Aug 2021 12:01:55 +0000
parents d2be2eb8350f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents: 3
diff changeset
1 <tool id="irods_download" name="iRODS Download" version="0.4" workflow_compatible="false">
2
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
2 <description>Download your files from iRODS into Galaxy</description>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
3 <requirements>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
4 <requirement type="package" version="0.8.2">python-irodsclient</requirement>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
5 </requirements>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
6
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
7 <command interpreter="python">
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
8 ### using CHEETAH ###
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
9 ## Set up iRODS params
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
10 #import json
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
11 #set params = {}
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
12 #set params["irods_host"] = str($custom_host)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
13 #set params["irods_port"] = str($custom_port)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
14 #set params["irods_zone"] = str($custom_zone)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
15 ##set params["filepath"] = str($file_path)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
16 #set params["file_path"] = str($file_path)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
17 ## set up Galaxy params
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
18 #set params["galaxy_user"] = str($__user_name__)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
19 #set params["job_id"] = str($output.creating_job.id)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
20 #set params["out_dir"] = str($output.files_path)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
21 #set params["out_file"] = str($output)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
22 #set params["galaxy_root"] = str($GALAXY_ROOT_DIR)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
23 #set params["galaxy_datatypes"] = str($GALAXY_DATATYPES_CONF_FILE)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
24 #set params["irods_user"] = str($user)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
25 #set params["irods_password"] = str($password)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
26 ##import os
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
27 ##import glob
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
28 ##set $test = glob.glob("os.getcwd()" + "/**/irods_galaxy_registry.xml", recursive=True)
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
29 ##set params["reg_file"]
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
30 #set params["tool_type"] = "down"
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
31 #set $params=json.dumps($params)
4
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents: 3
diff changeset
32 irods_main.py '$params'
2
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
33 </command>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
34
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
35 <inputs>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
36 <param name="custom_host" type="text" value="data.cyverse.tugraz.at" label="iRODS Host:" />
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
37 <param name="custom_port" type="text" value="1247" label="iRODS Port:" />
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
38 <param name="custom_zone" type="text" value="TUG" label="iRODS Zone:" />
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
39 <param name="file_path" type="text" value="E.g.: /ZONE/home/USER/my_data.txt" label="Path to iRODS File or Directory:" />
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
40 <param name="user" type="text" value="" label="iRODS User:" />
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
41 <param name="password" type="text" value="" label="iRODS Password:" />
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
42 </inputs>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
43
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
44 <outputs>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
45 <data name="output" label="${tool.name}: ${file_path}" auto_format="true" />
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
46 </outputs>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
47
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
48 <help>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
49 Download iRODS
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
50
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
51 </help>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
52 <citations>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
53 <citation type="bibtex">
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
54 @misc{Download-iRODS,
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
55 author = {Hohensinner, Richard},
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
56 year = {2021},
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
57 title = {iRODSTools},
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
58 publisher = {GitLab},
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
59 journal = {GitLab repository},
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
60 url = {https://gitlab.tugraz.at/D463A320ED7901AB/galaxy_irods_tools},
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
61 }
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
62 </citation>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
63 </citations>
0641ea2f75b1 "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
64 </tool>