Galaxy Tool Basics

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# Intro to Galaxy Tools

slides by @martenson

.footnote[\#usegalaxy / @galaxyproject]

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## Please Interrupt!

We want and will answer your questions.

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# The Problem

> You have written a Python script to analyze data and you want to share it with command-line averse colleagues

# The Solution

Integrate the script as a tool into (your) Galaxy server.

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# Requirements

* Have or write command line executable.
* Determine inputs and outputs of the tool.
* Describe the tool to Galaxy.
* Instruct Galaxy to load the tool.

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# What is a Galaxy tool?

- Set of resources that describes how to display and execute software.
- Cornerstone of Galaxy tool is a `tool wrapper` written in XML.
- Galaxy loads tools from configuration files (also XML).
  - The basic one is `tool_conf.xml`.
- The `tool_path` in `galaxy.ini` specifies filesystem path where to search for tools (defaults to `tools/`).

???
Wrapper can be written in .yml also.

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# Tool Syntax

The XML wrapper follows a [schema](https://docs.galaxyproject.org/en/latest/dev/schema.html).

simplified:
  * requirements
  * command
  * inputs
  * outputs
  * test
  * help
  * citation

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# Tool example (hashing tool)

```xml
<tool id="secure_hash_message_digest" name="Secure Hash / Message Digest" version="0.0.1">
    <description>on a dataset</description>
    <command interpreter="python">secure_hash_message_digest.py --input "${input1}" --output "${out_file1}"
        #if $algorithms.value:
            #for $algorithm in str( $algorithms ).split( "," ):
                --algorithm "${algorithm}"
            #end for
        #end if
    </command>
    <inputs>
        <param format="data" name="input1" type="data" label="Text file"/>
        <param name="algorithms" type="select" multiple="True" display="checkboxes" label="Choose the algorithms">
          <option value="md5"/>
          <option value="sha1"/>
          <option value="sha224"/>
          <option value="sha256"/>
          <option value="sha384"/>
          <option value="sha512"/>
          <validator type="no_options" message="You must select at least one algorithm." />
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="out_file1"/>
    </outputs>
</tool>
```

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# Tool example (hashing tool)

You need few more things:
- Add the wrapper to the `tools/` folder.
- Add script `secure_hash_message_digest.py` to the same folder.
- Add the following `<tool file="secure_hash_message_digest.xml" />` to the `tool_conf.xml`.
- Restart Galaxy.

???
If you use `<toolbox monitor="true">` you do not have to restart Galaxy for the tool to load.

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# Planemo

[Command-line utilities](http://planemo.readthedocs.io/) to ease the development of tools.

```shell
$ planemo lint
$ planemo test
$ planemo serve
```
[Full list of commands](http://planemo.readthedocs.io/en/latest/commands.html)

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# Building a tool using Planemo

This time connect with
```
ssh -L 9090:localhost:9090 galaxyguest@YOUR_VM
```

and then run
```
sudo apt-get install seqtk
```

Please follow the exercise at [Planemo documentation](http://planemo.readthedocs.io/en/latest/writing_standalone.html).