Mercurial > repos > tomnl > submit_to_mogi

annotate submit_to_mogi.xml @ 6:187641a876b9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875-dirty
author tomnl
date Tue, 28 Aug 2018 07:40:50 -0400
parents 821627b6ad6f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
187641a876b9 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875-dirty
tomnl
parents: 5
diff changeset
1 <tool id="submit_to_mogi" name="submit_to_mogi" version="0.0.3">
0
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
2 <description>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
3 Submit Galaxy datasets to MOGI django database
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
4 </description>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
5
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
6
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
7 <macros>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
8 <import>macros.xml</import>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
9 </macros>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
10
6
187641a876b9 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875-dirty
tomnl
parents: 5
diff changeset
11
0
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
12 <stdio>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
13 <exit_code range="1:" />
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
14 </stdio>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
15 <command>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
16 #set $galaxy_data_id=$__app__.security.encode_id($mogi_data.id)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
17 #set $galaxy_history_id=$__app__.security.encode_id($mogi_data.creating_job.history.id)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
18 #set $galaxy_history_name=$mogi_data.creating_job.history.name
5
821627b6ad6f planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875-dirty
tomnl
parents: 0
diff changeset
19 curl -X POST --insecure $mogi_url/mogi/rest/incoming_galaxy_data/ -d galaxy_data_id=$galaxy_data_id
0
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
20 -d galaxy_history_id=$galaxy_history_id -d galaxy_history_name='$galaxy_history_name'
5
821627b6ad6f planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875-dirty
tomnl
parents: 0
diff changeset
21 -d galaxy_name=$galaxy_name -d investigation_name=$investigation_name -d galaxy_url=$galaxy_url > curl_out.txt;
0
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
22 </command>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
23 <inputs>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
24
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
25
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
26 <param type="data" name="mogi_data" label="Data to submit to MOGI" format="sqlite"
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
27 help="SQLite database to submit to MOGI" />
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
28
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
29
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
30 <param type="text" name="mogi_url" label="MOGI URL"
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
31 help="URL for MOGI" />
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
32
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
33 <param type="text" name="galaxy_name" label="Name of Galaxy instance in MOGI"
5
821627b6ad6f planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875-dirty
tomnl
parents: 0
diff changeset
34 help="Should be lower cases with no white spaces or non alphnumeric characters except _ or -" />
821627b6ad6f planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875-dirty
tomnl
parents: 0
diff changeset
35
821627b6ad6f planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875-dirty
tomnl
parents: 0
diff changeset
36 <param type="text" name="investigation_name" label="Name of the investigation in submit to in MOGI"
821627b6ad6f planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875-dirty
tomnl
parents: 0
diff changeset
37 help="Should be lower cases with no white spaces or non alphnumeric characters except _ or -" />
0
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
38
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
39 <param type="text" name="galaxy_url" label="Galaxy URL"
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
40 help="URL of the Galaxy site (not required, but useful for a reference)" />
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
41
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
42
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
43
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
44 </inputs>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
45 <outputs>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
46 <data name="curl_out" format="json" label="${tool.name} on ${on_string}: submit to MOGI (json if successful)"
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
47 from_work_dir="curl_out.txt" />
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
48
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
49 </outputs>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
50 <tests>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
51 <test>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
52
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
53 <param name="mogi_data" value="alldata.sqlite"/>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
54 <param name="mogi_url" value="https://www.djangoproject.com/"/>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
55
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
56 <output name="curl_out" >
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
57 <assert_contents>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
58 <has_text_matching expression=".*django.*" />
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
59 </assert_contents>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
60 </output>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
61 </test>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
62 </tests>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
63
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
64 <help><![CDATA[
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
65 =============================================================
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
66 Submit SQLite Database to MOGI
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
67 =============================================================
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
68
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
69
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
70 -----------
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
71 Output
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
72 -----------
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
73 * out.json: The JSON request sent to MOGI
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
74
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
75 ]]></help>
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
76 <expand macro="citations" />
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
77 </tool>