Mercurial > repos > yating-l > gonramp_apollo

comparison jbrowsehubToApollo.xml @ 0:cb8439d64ed3 draft default tip

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planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
author yating-l
date Mon, 27 Nov 2017 14:40:53 -0500
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-1:000000000000 0:cb8439d64ed3
1 <tool id="jbrowsehubtoapollo" name="JBrowseHub To Apollo" version="1.0.0">
2 <description>
3 This Galaxy tool is used to prepare your files to be ready for displaying on Apollo
4 </description>
5
6 <requirements>
7 <requirement type="package" version="3.0.3">apollo_api</requirement>
8 </requirements>
9
10 <stdio>
11 </stdio>
12
13 <command detect_errors="exit_code"><![CDATA[
14
15 ## Dump the tool parameters into a JSON file
16 python $json_file parameters.json;
17 python $__tool_directory__/jbrowsehubToApollo.py --data_json parameters.json -o $output
18 ]]></command>
19 <configfiles>
20 <configfile name="json_file">
21 import json
22 import sys
23
24 file_path = sys.argv[1]
25 #set global data_parameter_dict = {}
26 #silent $data_parameter_dict.update({"action": str($action)})
27 #silent $data_parameter_dict.update({"species_name": str($species_name)})
28 #set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)}
29 #silent $data_parameter_dict.update({"apollo_admin": $apollo_admin})
30 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
31 #silent $data_parameter_dict.update({"extra_files_path": str($jbrowse_hub.extra_files_path)})
32 #silent $data_parameter_dict.update({"port": str($advanced_options.port)})
33 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
34 with open(file_path, 'w') as f:
35 json.dump($data_parameter_dict, f)
36 </configfile>
37 </configfiles>
38
39
40 <inputs>
41 <param
42 format="jbrowsehub"
43 type="data"
44 name="jbrowse_hub"
45 label="JBrowse Hub created by JBrowse Archive Creator"
46 />
47
48 <param name="action" type="select" label="Choose to create a new organism or overwrite an organism">
49 <option value="add" selected="true">Add a new organism to Apollo</option>
50 <option value="overwrite">Overwrite an existing organism on Apollo</option>
51 </param>
52
53 <param
54 name="species_name"
55 type="text"
56 size="30"
57 value="unknown"
58 label="Species name"
59 />
60
61 <param name="admin_username" type="text" label="Admin username" help="Login in with Apollo admin account">
62 <sanitizer>
63 <valid initial="string.letters,string.digits">
64 <add value="@-=_.()/+*^,:?!"/>
65 </valid>
66 </sanitizer>
67 </param>
68
69 <param
70 name="admin_password"
71 type="text"
72 label="Admin password"
73 />
74
75 <conditional name="advanced_options">
76 <param name="advanced_options_selector" type="select" label="Advanced options">
77 <option value="off" selected="true">Hide advanced options</option>
78 <option value="on">Display advanced options</option>
79 </param>
80 <!-- TODO: Avoid redundancy here -->
81 <when value="on">
82 <param name="port" type="integer" min="8000" max="8888" value="8080" label="Port number of Apollo" />
83 <param name="debug_mode" type="select" label="Activate debug mode">
84 <option value="false" selected="true">No</option>
85 <option value="true">Yes</option>
86 <help>
87 Use this option if you are a G-OnRamp developer
88 </help>
89 </param>
90 </when>
91 <when value="off">
92 <param name="port" type="hidden" value="8080" />
93 <param name="debug_mode" type="hidden"
94 value="false">
95 </param>
96 </when>
97 </conditional>
98 </inputs>
99 <outputs>
100 <data format="html" name="output" label="${tool.name}" />
101 </outputs>
102
103 <help>
104 This Galaxy tool is used to create or overwrite an organism on an Apollo server with a jbrowse hub created by JBrowse Archive Creator.
105 </help>
106 <citations>
107 </citations>
108 </tool>