annotate plot_barplot.xml @ 0:a8e03ffaaedc draft

planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 74beefba9d138c892208b103b52e706ab4313a4a-dirty

<tool id="plot_barplot" name="Plot barplot" 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__/plot_barplot.R
            --input_file $input_file
            --header $header

            #if str($output_format)=="pdf"
                --output_pdf_file $output_pdf_file
            #else
                --output_svg_file $output_svg_file
            #end if


            --data_column $column_with_data
            --names_column $names_column
            --xlab "$xlab"
            --col $col
            --bottom_margin $bottom_margin
            --left_margin $left_margin
            --top_margin $top_margin
            --right_margin $right_margin
    ]]></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="output_format" label="Format for output image" type="select" help="">
            <option value="pdf" selected="True">PDF</option>
            <option value="svg">SVG</option>
        </param>

        <param name="column_with_data" type="data_column" data_ref="input_file" multiple="false" numerical="true" label="Column containing data?" help="(--data_column)" />

        <param name="names_column" type="data_column" data_ref="input_file" multiple="false" numerical="false" label="Column containing data names?" help="(--names_column)" />

        <param name="xlab" type="text" value="" label="Label for x axis" help="(--xlab)"/>

        <param name="col" label="Bar color" type="text" value= "blue" help="R color (--col)"/>

        <param name="bottom_margin" type="integer" value="5" label="Bottom margin" help="(--bottom_margin)"/>
        <param name="left_margin" type="integer" value="19" label="Left margin" help="(--left_margin)"/>
        <param name="top_margin" type="integer" value="1" label="Top margin" help="(--top_margin)"/>
        <param name="right_margin" type="integer" value="1" label="Right margin" help="(--right_margin)"/>
    </inputs>

    <outputs>
        <data name="output_pdf_file" format="pdf"
            label="${tool.name} on ${on_string}: PDF barplot">
            <filter>output_format=="pdf"</filter>
        </data>
        <data name="output_png_file" format="png"
            label="${tool.name} on ${on_string}: PNG barplot">
            <filter>output_format=="png"</filter>
        </data>
        <data name="output_svg_file" format="svg"
            label="${tool.name} on ${on_string}: SVG barplot">
            <filter>output_format=="svg"</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="input_file" value="input_file.txt"/>
            <param name="header" value="FALSE"/>
            <param name="output_format" value="pdf"/>
            <param name="column_with_data" value="2"/>
            <param name="names_column" value="1"/>
            <param name="xlab" value=""/>
            <param name="col" value="blue"/>
            <param name="bottom_margin" value="5"/>
            <param name="left_margin" value="19"/>
            <param name="top_margin" value="1"/>
            <param name="right_margin" value="1"/>
            <output name="output_pdf_file" file="output_test_col_2.pdf"/>
        </test>
        <test>
            <param name="input_file" value="input_file.txt"/>
            <param name="header" value="FALSE"/>
            <param name="output_format" value="pdf"/>
            <param name="column_with_data" value="3"/>
            <param name="names_column" value="1"/>
            <param name="xlab" value=""/>
            <param name="col" value="red"/>
            <param name="bottom_margin" value="5"/>
            <param name="left_margin" value="19"/>
            <param name="top_margin" value="1"/>
            <param name="right_margin" value="1"/>
            <output name="output_pdf_file" file="output_test_col_3.pdf"/>
        </test>
    </tests>

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

This tool plot a barplot.

.. image:: $PATH_TO_IMAGES/output.png
   :scale: 50 %

This tool relies on R's barplot function. The input file must be a tabular file with multiple columns: a column with row names (for bar names) and a least a column with data. The output image is customizable (margin, legend positions, ...) and can be export in different format. 
    ]]></help>

    <citations>
    </citations>
</tool>