inst/extdata/README.md

In MingChen0919/elagator: Assist in developing ELAstic GAlaxy TOols in R

Dynamic Galaxy Tool wrappers

Use this repository as a template to develop a elastic Galaxy tools in one minute!

Step 1: clone this repository

git clone https://github.com/statonlab/elastic-galaxy-tool-wrappers.git

Step 2: edit tool requirements

Open the elastic_tool_wrappers_macros.xml file and add your tool requirements. Only tools from the conda repository can be added as a tool requirement. For example, for a wrapper of the FastQC** tool, go to https://anaconda.org/anaconda/repo and search for fastqc. You will get a list of fastqc tools. Find the appropriate version and add it as a tool requirement.

Before editing tool requirement:

    <xml name="rmarkdown_requirements">
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.6">r-rmarkdown</requirement>
    </xml>

After editing tool requirement:

    <xml name="rmarkdown_requirements">
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.6">r-rmarkdown</requirement>
        <requirement type="package" version="0.11.7">fastqc</requirement>
    </xml>

Step 3: edit template for a specific command line tool

Open the elastic_tool_wrappers_macros.xml file and replace tool_name in <option value="tool_name" selected="false">tool_name</option> with a valid command line tool name.

    <xml name="tool_name">
        <param type="select" name="tool_name" multiple="false" label="Tool name">
            <option value="tool_name" selected="false">tool_name</option>
        </param>
    </xml>

Use the FastQC tool as an example again, the content after replacement would be

    <xml name="tool_name">
        <param type="select" name="tool_name" multiple="false" label="Tool name">
            <option value="fastqc" selected="false">fastqc</option>
        </param>
    </xml>

You can add multiple tool_name options if the tool has sub command line tools. For example, for the samtools tool, it could be

    <xml name="tool_name">
        <param type="select" name="tool_name" multiple="false" label="Tool name">
            <option value="samtools view" selected="false">samtols view</option>
            <option value="samtools sort" selected="false">samtols sort</option>
            <option value="samtools index" selected="false">samtols index</option>
        </param>
    </xml>

Step 4: edit tool name and tool id in elastic_tool.xml

Open the elastic_tool.xml file and replace elastic_tool with an appropriate tool id and the elastic tool with an appropriate tool name.

<tool id="elastic_tool" name="elastic tool" version="1.0.0">

Use the FastQC tool as an example, it could be:

<tool id="elastic_fastqc" name="Dynamic FastQC" version="1.0.0">

Step 5: Publish tool to ToolShed or Test ToolShed

Please check planemo's documentation site for more details.

• Within the tool directory, planemo shed_init command can be used to bootstrap a .shed.yml file.

planemo shed_init --name=<name>
                  --owner=<shed_username>
                  --description=<short description>
                  [--remote_repository_url=<URL to .shed.yml on github>]
                  [--homepage_url=<Homepage for tool.>]
                  [--long_description=<long description>]
                  [--category=<category name>]*

• Create tool repository on ToolShed or Test ToolShed

planemo shed_create --shed_target testtoolshed

• Update a tool repository

planemo shed_diff --shed_target testtoolshed

MingChen0919/elagator documentation built on May 17, 2019, 6:22 p.m.