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comparison jbrowsehubToApollo.xml @ 0:ce4f91831680 draft default tip

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planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894
author yating-l
date Fri, 16 Feb 2018 10:57:13 -0500
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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 mkdir -p $output.extra_files_path;
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 $data_parameter_dict.update({"action": str($action)})
28 #silent $data_parameter_dict.update({"species_name": str($species_name)})
29 #set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)}
30 #silent $data_parameter_dict.update({"apollo_admin": $apollo_admin})
31 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
32 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
33 #slient $data_parameter_dict.update({"jbrowse_hub": str($jbrowse_hub.extra_files_path)})
34 #silent $data_parameter_dict.update({"port": str($advanced_options.port)})
35 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
36 with open(file_path, 'w') as f:
37 json.dump($data_parameter_dict, f)
38 </configfile>
39 </configfiles>
40
41
42 <inputs>
43 <param
44 format="jbrowsehub"
45 type="data"
46 name="jbrowse_hub"
47 label="JBrowse Hub created by JBrowse Archive Creator"
48 />
49
50 <param name="action" type="select" label="Choose to create a new organism or overwrite an organism">
51 <option value="add" selected="true">Add a new organism to Apollo</option>
52 <option value="overwrite">Overwrite an existing organism on Apollo</option>
53 </param>
54
55 <param
56 name="species_name"
57 type="text"
58 size="30"
59 value="unknown"
60 label="Species name"
61 />
62
63 <param name="admin_username" type="text" label="Admin username" help="Login in with Apollo admin account">
64 <sanitizer>
65 <valid initial="string.letters,string.digits">
66 <add value="@-=_.()/+*^,:?!"/>
67 </valid>
68 </sanitizer>
69 </param>
70
71 <param
72 name="admin_password"
73 type="text"
74 label="Admin password"
75 />
76
77 <conditional name="advanced_options">
78 <param name="advanced_options_selector" type="select" label="Advanced options">
79 <option value="off" selected="true">Hide advanced options</option>
80 <option value="on">Display advanced options</option>
81 </param>
82 <!-- TODO: Avoid redundancy here -->
83 <when value="on">
84 <param name="port" type="integer" min="8000" max="8888" value="8080" label="Port number of Apollo" />
85 <param name="debug_mode" type="select" label="Activate debug mode">
86 <option value="false" selected="true">No</option>
87 <option value="true">Yes</option>
88 <help>
89 Use this option if you are a G-OnRamp developer
90 </help>
91 </param>
92 </when>
93 <when value="off">
94 <param name="port" type="hidden" value="8080" />
95 <param name="debug_mode" type="hidden"
96 value="false">
97 </param>
98 </when>
99 </conditional>
100 </inputs>
101 <outputs>
102 <data format="html" name="output" label="${tool.name}" />
103 </outputs>
104
105 <help>
106 This Galaxy tool is used to create or overwrite an organism on an Apollo server with a jbrowse hub created by JBrowse Archive Creator.
107 </help>
108 <citations>
109 </citations>
110 </tool>