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1 # Dynamic Galaxy Tool wrappers
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2
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3 Use this repository as a template to develop a dynamic Galaxy tools in one minute!
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4
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5 ## Step 1: clone this repository
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6
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7 ```bash
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8 git clone https://github.com/statonlab/dynamic-galaxy-tool-wrappers.git
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9 ```
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10
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11 ## Step 2: edit tool requirements
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12
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13 Open the `dynamic_tool_wrappers_macros.xml` file and add your tool requirements. **Only tools from the
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14 [conda repository](https://anaconda.org/anaconda/repo) can be added as a tool requirement. For example, for a wrapper
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15 of the **FastQC** tool, go to [https://anaconda.org/anaconda/repo](https://anaconda.org/anaconda/repo) and search for
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16 `fastqc`. You will get a list of `fastqc` tools. Find the appropriate version and add it as a tool requirement.
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17
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18 Before editing tool requirement:
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19
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20 ```xml
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21 <xml name="rmarkdown_requirements">
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22 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
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23 <requirement type="package" version="1.6">r-rmarkdown</requirement>
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24 </xml>
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25 ```
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26
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27 After editing tool requirement:
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28
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29 ```xml
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30 <xml name="rmarkdown_requirements">
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31 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
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32 <requirement type="package" version="1.6">r-rmarkdown</requirement>
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33 <requirement type="package" version="0.11.7">fastqc</requirement>
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34 </xml>
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35 ```
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36
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37
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38
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39 ## Step 3: edit template for a specific command line tool
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40
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41 Open the `dynamic_tool_wrappers_macros.xml` file and replace `tool_name` in
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42 `<option value="tool_name" selected="false">tool_name</option>` with a valid command line tool name.
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43
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44 ```xml
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45 <xml name="tool_name">
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46 <param type="select" name="tool_name" multiple="false" label="Tool name">
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47 <option value="tool_name" selected="false">tool_name</option>
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48 </param>
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49 </xml>
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50 ```
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51
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52 Use the **FastQC** tool as an example again, the content after replacement would be
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53
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54 ```xml
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55 <xml name="tool_name">
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56 <param type="select" name="tool_name" multiple="false" label="Tool name">
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57 <option value="fastqc" selected="false">fastqc</option>
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58 </param>
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59 </xml>
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60 ```
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61
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62 You can add multiple `tool_name` options if the tool has sub command line tools. For example,
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63 for the `samtools` tool, it could be
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64
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65 ```xml
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66 <xml name="tool_name">
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67 <param type="select" name="tool_name" multiple="false" label="Tool name">
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68 <option value="samtools view" selected="false">samtols view</option>
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69 <option value="samtools sort" selected="false">samtols sort</option>
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70 <option value="samtools index" selected="false">samtols index</option>
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71 </param>
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72 </xml>
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73 ```
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74
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75 ## Step 4: edit **tool name** and **tool id** in `dynamic_tool.xml`
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76
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77 Open the `dynamic_tool.xml` file and replace `dynamic_tool` with an appropriate **tool id** and the `dynamic tool` with
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78 an appropriate **tool name**.
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79
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80 ```xml
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81 <tool id="dynamic_tool" name="dynamic tool" version="1.0.0">
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82 ```
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83
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84 Use the **FastQC** tool as an example, it could be:
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85
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86 ```xml
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87 <tool id="dynamic_fastqc" name="Dynamic FastQC" version="1.0.0">
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88 ```
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89
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90 ## Step 5: Publish tool to [ToolShed](https://toolshed.g2.bx.psu.edu/) or [Test ToolShed](https://testtoolshed.g2.bx.psu.edu/)
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91
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92 Please check [planemo's documentation site](http://planemo.readthedocs.io/en/latest/publishing.html) for more details.
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93
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94 * Within the tool directory, `planemo shed_init` command can be used to bootstrap a `.shed.yml` file.
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95
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96 ```bash
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97 planemo shed_init --name=<name>
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98 --owner=<shed_username>
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99 --description=<short description>
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100 [--remote_repository_url=<URL to .shed.yml on github>]
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101 [--homepage_url=<Homepage for tool.>]
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102 [--long_description=<long description>]
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103 [--category=<category name>]*
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104 ```
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105
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106 * **Create tool repository on ToolShed or Test ToolShed**
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107
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108 ```bash
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109 planemo shed_create --shed_target testtoolshed
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110 ```
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111
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112 * **Update a tool repository**
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113
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114 ```bash
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115 planemo shed_diff --shed_target testtoolshed
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116 ``` |
