annotate compute_wilcoxon_test.xml @ 0:2a8acb4c0afc draft default tip

planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646

<tool id="compute_wilcoxon_test" name="Compute Wilcoxon test" version="0.1.0">
    <description>with R</description>

    <requirements>
        <requirement type="package" version="3.2.1">R</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>

    <version_command></version_command>

    <command><![CDATA[
        Rscript $__tool_directory__/compute_wilcoxon_test.R
            --input_file $input_file
	    --header $header
            --output_file $output_file
            --column1_id $column1_id

            #if $add_column.add_column_test == "true":
                --column2_id $add_column.column2_id
                --paired $add_column.paired
            #end if

            --alternative "$alternative"
            --mu $mu
            
            --exact $exact
            --correct $correct
            
    ]]></command>

    <inputs>
        <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/>

        <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/>
  
        <param name="column1_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column1_id)"/>

        <conditional name="add_column">
            <param name="add_column_test" label="Add a new column?" type="select" help="(--alternative)">
                <option value="true" selected="true">Yes</option>
                <option value="false">No</option>
            </param>
            <when value="true">
                <param name="column2_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column2_id)"/>
                <param name="paired" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Paired datasets?" checked="false" help="(--paired)"/>
            </when>
            <when value="false" />
        </conditional>

        <param name="alternative" label="Alternative hypothesis" type="select" help="(--alternative)">
            <option value="two.sided" selected="true">Two sided</option>
            <option value="greater">Greater</option>
            <option value="less">Less</option>
        </param>
        <param name="mu" type="integer" value="0" label="Optional parameter used to form the null hypothesis" help="(--mu)"/>
        
        <param name="exact" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Compute an exact p-value?" checked="false" help="(--exact)"/>
        <param name="correct" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Apply a continuity correction in the normal approximation for the p-value?" checked="true" help="(--correct)"/>
    </inputs>

    <outputs>
        <data name="output_file" format="txt"  label="${tool.name} on ${on_string}: Wilcox test result" />
    </outputs>

    <tests>
        <test>
            <param name="input_file" ftype="tabular" value="input_file.txt"/>
            <param name="header" value="TRUE"/>
            <param name="column1_id" value="3"/>
            <param name="add_column_test" value="true"/>
            <param name="column2_id" value="5"/>
            <param name="paired" value="FALSE"/>
            <param name="alternative" value="two.sided"/>
            <param name="mu" value="0"/>
            <param name="exact" value="FALSE"/>
            <param name="correct" value="TRUE"/>
            <output name="output_file" file="two_sided_two_columns_test_output.txt"/>
        </test>
    </tests>

    <help><![CDATA[
**What it does**

This tool compute a Wilcoxon test with R's wilcox.test function.
    ]]></help>

    <citations>
    </citations>
</tool>