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comparison submit_to_mogi.xml @ 5:821627b6ad6f draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875-dirty
author tomnl
date Tue, 28 Aug 2018 07:13:51 -0400
parents 58ee3687f776
children 187641a876b9
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4:4de1b44b4c5e 5:821627b6ad6f
1 <tool id="submit_to_mogi" name="submit_to_mogi" version="0.0.1"> 1 <tool id="submit_to_mogi" name="submit_to_mogi" version="0.0.2">
2 <description> 2 <description>
3 Submit Galaxy datasets to MOGI django database 3 Submit Galaxy datasets to MOGI django database
4 </description> 4 </description>
5 5
6 6
18 </stdio> 18 </stdio>
19 <command> 19 <command>
20 #set $galaxy_data_id=$__app__.security.encode_id($mogi_data.id) 20 #set $galaxy_data_id=$__app__.security.encode_id($mogi_data.id)
21 #set $galaxy_history_id=$__app__.security.encode_id($mogi_data.creating_job.history.id) 21 #set $galaxy_history_id=$__app__.security.encode_id($mogi_data.creating_job.history.id)
22 #set $galaxy_history_name=$mogi_data.creating_job.history.name 22 #set $galaxy_history_name=$mogi_data.creating_job.history.name
23 curl -X POST --insecure $mogi_url/rest/incoming_galaxy_data/ -d galaxy_data_id=$galaxy_data_id 23 curl -X POST --insecure $mogi_url/mogi/rest/incoming_galaxy_data/ -d galaxy_data_id=$galaxy_data_id
24 -d galaxy_history_id=$galaxy_history_id -d galaxy_history_name='$galaxy_history_name' 24 -d galaxy_history_id=$galaxy_history_id -d galaxy_history_name='$galaxy_history_name'
25 -d galaxy_name=$galaxy_name -d galaxy_url=$galaxy_url > curl_out.txt; 25 -d galaxy_name=$galaxy_name -d investigation_name=$investigation_name -d galaxy_url=$galaxy_url > curl_out.txt;
26 </command> 26 </command>
27 <inputs> 27 <inputs>
28 28
29 29
30 <param type="data" name="mogi_data" label="Data to submit to MOGI" format="sqlite" 30 <param type="data" name="mogi_data" label="Data to submit to MOGI" format="sqlite"
33 33
34 <param type="text" name="mogi_url" label="MOGI URL" 34 <param type="text" name="mogi_url" label="MOGI URL"
35 help="URL for MOGI" /> 35 help="URL for MOGI" />
36 36
37 <param type="text" name="galaxy_name" label="Name of Galaxy instance in MOGI" 37 <param type="text" name="galaxy_name" label="Name of Galaxy instance in MOGI"
38 help="Should be lower cases with no white spaces or non alphnumeric characters" /> 38 help="Should be lower cases with no white spaces or non alphnumeric characters except _ or -" />
39
40 <param type="text" name="investigation_name" label="Name of the investigation in submit to in MOGI"
41 help="Should be lower cases with no white spaces or non alphnumeric characters except _ or -" />
39 42
40 <param type="text" name="galaxy_url" label="Galaxy URL" 43 <param type="text" name="galaxy_url" label="Galaxy URL"
41 help="URL of the Galaxy site (not required, but useful for a reference)" /> 44 help="URL of the Galaxy site (not required, but useful for a reference)" />
42 45
43 46