Mercurial > repos > rhohensinner > galaxy_irods_interface
comparison 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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1:19c1cecdfdfd | 2:0641ea2f75b1 |
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1 <tool id="irods_upload" name="iRODS Upload" version="0.2" workflow_compatible="false"> | |
2 <description>Upload your files to iRODS from 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 #import json | |
10 #set params = {} | |
11 #set params["irods_host"] = str($custom_host) | |
12 #set params["irods_port"] = str($custom_port) | |
13 #set params["irods_zone"] = str($custom_zone) | |
14 ##if $irods_config.typeiRODS == "use_any_irods" | |
15 ##set params["irods_host"] = str($irods_config.custom_host) | |
16 ##set params["irods_port"] = str($irods_config.custom_port) | |
17 ##set params["irods_zone"] = str($irods_config.custom_zone) | |
18 ##end if | |
19 ##if $irods_config.typeiRODS == "use_tug_irods" | |
20 ##set params["irods_host"] = "data.cyverse.tugraz.at" | |
21 ##set params["irods_port"] = "1247" | |
22 ##set params["irods_zone"] = "TUG" | |
23 ##end if | |
24 ## set up Galaxy params | |
25 #set params["galaxy_user"] = str($__user_name__) | |
26 #set params["job_id"] = str($output.creating_job.id) | |
27 #set params["out_dir"] = str($output.files_path) | |
28 #set params["out_file"] = str($output) | |
29 #set params["up_file"] = str($up_file.name) | |
30 #set params["up_file_path"] = str($up_file) | |
31 #set params["galaxy_root"] = str($GALAXY_ROOT_DIR) | |
32 #set params["galaxy_datatypes"] = str($GALAXY_DATATYPES_CONF_FILE) | |
33 #set params["tool_type"] = "up" | |
34 #set params["irods_user"] = str($user) | |
35 #set params["irods_password"] = str($password) | |
36 #set $params=json.dumps($params) | |
37 main.py '$params' | |
38 </command> | |
39 | |
40 <inputs> | |
41 <param name="custom_host" type="text" value="data.cyverse.tugraz.at" label="iRODS Host:" /> | |
42 <param name="custom_port" type="text" value="1247" label="iRODS Port:" /> | |
43 <param name="custom_zone" type="text" value="TUG" label="iRODS Zone:" /> | |
44 <param name="up_file" type="data" value="" label="Galaxy file to upload" /> | |
45 <param name="user" type="text" value="" label="iRODS User:" /> | |
46 <param name="password" type="text" value="" label="iRODS Password:" /> | |
47 | |
48 </inputs> | |
49 | |
50 <outputs> | |
51 <data name="output" auto_format="true" /> | |
52 </outputs> | |
53 | |
54 <help> | |
55 Upload RODS | |
56 | |
57 </help> | |
58 <citations> | |
59 <citation type="bibtex"> | |
60 @misc{Upload-iRODS, | |
61 author = {Hohensinner, Richard}, | |
62 year = {2021}, | |
63 title = {iRODSTools}, | |
64 publisher = {GitLab}, | |
65 journal = {GitLab repository}, | |
66 url = {https://gitlab.tugraz.at/D463A320ED7901AB/galaxy_irods_tools}, | |
67 } | |
68 </citation> | |
69 </citations> | |
70 </tool> |