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1 # Elastic Galaxy Tools
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2
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3 * [What are Elastic Galaxy Tools](#what-are-elastic-galaxy-tools?)
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4 * [How to use Elastic Galaxy Tools](#how-to-use-elastic-galaxy-tools?)
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5 * [How to develop an Elastic Galaxy Tool](#how-to-develop-an-elastic-galaxy-tool?)
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6 + [Publish a Galaxy Tool](#publish-a-galaxy-tool)
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7
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8
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9
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10
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11 ## What are Elastic Galaxy Tools?
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12
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13 **Elastic Galaxy tools** is a type of Galaxy tools that have elastic user interfaces. Users can adjust the
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14 number of input fields a tool can have, just like using a command line tool. When using a command line tool,
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15 users can choose which (non-required) options to use. I hope Galaxy users can do the same thing, but without
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16 actually writing any command line scripts.
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17
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18
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19 ## How to use Elastic Galaxy Tools?
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20
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21 Although any (Elastic) Galaxy tool is a wrapper of a command line tool which enables performing data analysis
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22 through web interfaces without actually writing any command line script, understanding how to read command line
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23 manuals will help you use Elastic Galaxy tools.
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24
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25 Running a command line tool is very simple. You start with the tool name, then you specify options (also called flags)
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26 that the tool can recognize. The tool manual should tell you which options the tool can recognize. An option may or may
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27 not have a value followed. Some options are required and some are optional. You have to use all required options to
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28 successfully run a command line tool. However, you can use as many optional options as you want in a call of a command
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29 line tool.
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30
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31 ## How to develop an Elastic Galaxy Tool?
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32
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33 ### Publish a Galaxy tool
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34
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35 We can use the tool **planemo** to easily publish our Galaxy tools to Tool Shed or test Tool Shed.
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36 More details can be found **[here](http://planemo.readthedocs.io/en/latest/publishing.html)**.
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37
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38 * Publish to test Tool Shed
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39
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40 ```bash
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41 planemo shed_create --shed_target testtoolshed
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42 ```
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43
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44 * Update tool repository in test Tool Shed
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45
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46 ```bash
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47 planemo shed_update --check_diff --shed_target testtoolshed
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48 ```
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49
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50 * Publish to Tool Shed
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51
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52 ```bash
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53 planemo shed_create --shed_target toolshed
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54 ```
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55
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56 * Update tool repository in Tool Shed
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57
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58 ```bash
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59 planemo shed_update --check_diff --shed_target toolshed
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60 ```
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