annotate alpha_diversity.xml @ 2:dc7fd9e2d835 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit afc6220b1e5f402f872338bbab440e4a1fe04ccd

<tool id="krakentools_alpha_diversity" name="Krakentools: Calculates alpha diversity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>from the Bracken abundance estimation file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements">
        <requirement type="package" version="1.9.3">scipy</requirement>
    </expand>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
alpha_diversity.py 
    --filename '$filename'
    --alpha '$alpha'
    > '$output'
    ]]></command>
    <inputs>
        <param argument="--filename" type="data" format="tabular" label="Abundance file" help="The file can be created by Bracken"/>
        <param argument="--alpha" type="select" label="Specify alpha diversity type">
            <option value="Sh" selected="true">Shannon's alpha diversity</option>
            <option value="BP">Berger-Parker's alpha</option>
            <option value="Si">Simpson's diversity</option>
            <option value="ISi">Inverse Simpson's diversity</option>
            <option value="F">Fisher's index</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="filename" value="bracken_abundance.tabular"/>
            <param name="alpha" value="Sh"/>
            <output name="output" ftype="txt">
                <assert_contents>
                    <has_text text="Shannon's diversity: 4.194127607417342"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="filename" value="bracken_abundance.tabular"/>
            <param name="alpha" value="BP"/>
            <output name="output" ftype="txt">
                <assert_contents>
                    <has_text text="Berger-parker's diversity: 0.05525121757950085"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="filename" value="bracken_abundance.tabular"/>
            <param name="alpha" value="Si"/>
            <output name="output" ftype="txt">
                <assert_contents>
                    <has_text text="Simpson's diversity: 0.9805668888241948"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="filename" value="bracken_abundance.tabular"/>
            <param name="alpha" value="ISi"/>
            <output name="output" ftype="txt">
                <assert_contents>
                    <has_text text="Simpson's Reciprocal Index: 51.45856424909617"/>
                </assert_contents>
            </output>              
        </test>
        <test>
            <param name="filename" value="bracken_abundance.tabular"/>
            <param name="alpha" value="F"/>
            <output name="output" ftype="txt">
                <assert_contents>
                    <has_text text="Fisher's index: 1688.9352909860668"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs. These scripts are designed to help Kraken users with downstream analysis of Kraken results. This program calculates alpha diversity, from the Bracken abundance estimation file. User must specify Bracken output file, and type of alpha diversity to be calculated. Specific options are specified below.

Input
------
Bracken abundance estimation file.

Input Bracken file must be in standard Bracken output file format and must be run specifically for Abundance Estimation. Example format:
    name                     tax_id tax_lvl kraken... added... new...  fraction...
    Homo sapiens             9606   S       ...        ....    999000  0.999000
    Streptococcus pyogenes   1314   S       ...        ....    10      0.000001
    Streptococcus agalactiae 1311   S       ...        ....    5       0.000000
    Streptococcus pneumoniae 1313   S       ...        ....    3       0.000000
    Bordetella pertussis     520    S       ...        ....    20      0.000002

Output
---------
Alpha diversity with the specified type.

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