Mercurial > repos > yating-l > suite_gonramp_apollo2

annotate jbrowsehubToApollo.xml @ 0:9945eba268e6 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 12:49:27 -0500
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1 <tool id="jbrowsehubtoapollo" name="JBrowseHub To Apollo" version="1.0.0">
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2 <description>
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3 This Galaxy tool is used to prepare your files to be ready for displaying on Apollo
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4 </description>
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5
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6 <requirements>
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7 <requirement type="package" version="3.0.3">apollo_api</requirement>
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8 </requirements>
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9
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10 <stdio>
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11 </stdio>
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12
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13 <command detect_errors="exit_code"><![CDATA[
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14
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15 ## Dump the tool parameters into a JSON file
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16 python $json_file parameters.json;
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17 python $__tool_directory__/jbrowsehubToApollo.py --data_json parameters.json -o $output
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18 ]]></command>
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19 <configfiles>
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20 <configfile name="json_file">
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21 import json
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22 import sys
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23
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24 file_path = sys.argv[1]
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25 #set global data_parameter_dict = {}
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26 #silent $data_parameter_dict.update({"action": str($action)})
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27 #silent $data_parameter_dict.update({"species_name": str($species_name)})
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28 #set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)}
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29 #silent $data_parameter_dict.update({"apollo_admin": $apollo_admin})
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30 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
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31 #silent $data_parameter_dict.update({"extra_files_path": str($jbrowse_hub.extra_files_path)})
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32 #silent $data_parameter_dict.update({"port": str($advanced_options.port)})
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33 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
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34 with open(file_path, 'w') as f:
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35 json.dump($data_parameter_dict, f)
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36 </configfile>
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37 </configfiles>
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38
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39
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40 <inputs>
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41 <param
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42 format="jbrowsehub"
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43 type="data"
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44 name="jbrowse_hub"
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45 label="JBrowse Hub created by JBrowse Archive Creator"
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46 />
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47
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48 <param name="action" type="select" label="Choose to create a new organism or overwrite an organism">
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49 <option value="add" selected="true">Add a new organism to Apollo</option>
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50 <option value="overwrite">Overwrite an existing organism on Apollo</option>
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51 </param>
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52
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53 <param
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54 name="species_name"
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55 type="text"
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56 size="30"
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57 value="unknown"
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58 label="Species name"
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59 />
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60
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61 <param name="admin_username" type="text" label="Admin username" help="Login in with Apollo admin account">
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62 <sanitizer>
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63 <valid initial="string.letters,string.digits">
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64 <add value="@-=_.()/+*^,:?!"/>
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65 </valid>
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66 </sanitizer>
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67 </param>
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68
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69 <param
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70 name="admin_password"
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71 type="text"
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72 label="Admin password"
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73 />
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74
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75 <conditional name="advanced_options">
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76 <param name="advanced_options_selector" type="select" label="Advanced options">
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77 <option value="off" selected="true">Hide advanced options</option>
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78 <option value="on">Display advanced options</option>
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79 </param>
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80 <!-- TODO: Avoid redundancy here -->
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81 <when value="on">
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82 <param name="port" type="integer" min="8000" max="8888" value="8080" label="Port number of Apollo" />
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83 <param name="debug_mode" type="select" label="Activate debug mode">
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84 <option value="false" selected="true">No</option>
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85 <option value="true">Yes</option>
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86 <help>
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87 Use this option if you are a G-OnRamp developer
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88 </help>
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89 </param>
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90 </when>
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91 <when value="off">
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92 <param name="port" type="hidden" value="8080" />
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93 <param name="debug_mode" type="hidden"
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94 value="false">
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95 </param>
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96 </when>
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97 </conditional>
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98 </inputs>
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99 <outputs>
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100 <data format="html" name="output" label="${tool.name}" />
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101 </outputs>
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102
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103 <help>
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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.
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105 </help>
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106 <citations>
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107 </citations>
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108 </tool>