annotate snpEff_databases.xml @ 30:c7275bd8b4d6 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 280d5247becaa9a70db9c5c4a2f1fc50d302838a

<tool id="snpEff_databases" name="SnpEff databases:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <description> list available databases</description>
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <requirements>
        <expand macro="requirement" />
    </requirements>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        snpEff databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/  *//g'

        #if $include_pattern:
             | grep -e '^#' -e '${include_pattern}'
        #end if

        #if $exclude_pattern:
             | grep -v '${exclude_pattern}'
        #end if

        #if str($include_download_path) == "no":
            | cut -f 1,2,3,4
        #end if

        > '${snpeff_dbs}'
    ]]></command>
    <inputs>
        <param name="include_pattern" type="text" value="" optional="true" label="List entries matching the following expression" help="Databases matching this expression will be listed. Here you can enter text or regular expression. For example, to show only mouse databases use 'Mouse'. Note that this parameter is case-sensitive.">
            <sanitizer>
                <valid initial="string.digits,string.letters">
                    <add value="^" />
                    <add value="_" />
                </valid>
            </sanitizer>
        </param>
        <param name="exclude_pattern" type="text" value="" optional="true" label="Do not output entries matching the following expression" help="Databases matching this expression WILL NOT BE listed. Here you can enter text or regular expression. For excample, to avoid all ENSEMBL bundles enter 'ENSEMBL'. Note that this parameter is case-sensitive.">
            <sanitizer>
                <valid initial="string.digits,string.letters">
                    <add value="^" />
                    <add value="_" />
                </valid>
            </sanitizer>
        </param>
        <param name="include_download_path" type="select" display="radio" label="Include download paths?" help="When snpEff dumps the list of available databases, it includes their download paths. These are not needed in the Galaxy context.">
            <option value="yes">Yes</option>
            <option value="no" selected="true">No</option>
        </param>
    </inputs>
    <outputs>
        <data name="snpeff_dbs" format="tabular" label="@SNPEFF_VERSION@ available databases" />
    </outputs>
    <tests>
        <test>
            <output name="snpeff_dbs">
                <assert_contents>
                    <has_text text="ebola_zaire" />
                </assert_contents>
            </output>
        </test>
         <test>
            <param name="include_pattern" value="ebola"/>
            <output name="snpeff_dbs">
                <assert_contents>
                    <has_text text="ebola_zaire" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool downloads the master list of snpEff databases from a remote SnpEff repository. You can then look at this list and decide which database to use for your analysis. For example, if **List entries matching the following expression** parameter of this tool is set to *Mouse*, it will produce a tabular dataset with the following content::

    mm10  Mouse
    mm39  Mouse
    mm9   Mouse

This means that there are three available snpEff databases for mouse genome. If you want to use mm39 in you analysis:

 - set **Genome source** option of **SnpEff eff** Galaxy tool to *Download on demand*
 - enter 'mm39' into **Snpff Genome Version Name** text box

-------

.. class:: infomark

**The usage scenario**

There are two ways to use names of databases obtained with this tool in Galaxy's version on snpEff:

    #. Use **SnpEff download** tool. It will download the database to the history and you will be able to use it in **SnpEff eff** tool using *Downloaded snpEff database in your history* option of the **Genome source** parameter.
    #. Use *Download on demand* option of the **SnpEff eff** tool (again, **Genome source** parameter). In this case snpEff will download the database before performing annotation.

@SNPEFF_IN_GALAXY_INFO@
@EXTERNAL_DOCUMENTATION@

    ]]></help>
    <expand macro="citations" />
</tool>