annotate plot.xml @ 0:f370d221c284 draft default tip

"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"

<tool id="csvtk_plot" name="csvtk-plot" version="@VERSION@+@GALAXY_VERSION@">
    <description> histogram, line/scatter plot, or boxplot based on column</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_cmd" />
    <command detect_errors="exit_code"><![CDATA[

###################
## Start Command ##
###################
csvtk plot 

#if $plot_type.plot == "histogram"
    hist
#elif $plot_type.plot == "boxplot"
    box
#elif $plot_type.plot == "line"
    line
#end if

    --num-cpus "\${GALAXY_SLOTS:-1}"

    ## Add additional flags as specified ##
    #######################################
    $global_param.illegal_rows
    $global_param.empty_rows
    $global_param.header
    $global_param.lazy_quotes

    ## Set Tabular input/output flag if first input is tabular ##
    #############################################################
    #if $in_1.is_of_type("tabular"):
        -t -T
    #end if

    ## Set input files ##
    #####################
    $in_1

    ## Specific Plot Parameters ##
    ##############################
    #if $plot_type.plot == "histogram"
        -f '$plot_type.column_text.in_text'
        --color-index $plot_type.colour

    #elif $plot_type.plot == "boxplot"
        -f '$plot_type.column_text.in_text'
        $plot_type.horizontal

        #if $plot_type.group_field.select_group != "none"
            -g '$plot_type.group_field.in_text'
        #end if

        #if $plot_type.box_width
            --box-width '$plot_type.box_width'
        #end if

    #elif $plot_type.plot == "line"
        $plot_type.scatter
        -x '$plot_type.column_text.in_text_x'
        -y '$plot_type.column_text.in_text_y'

        #if $plot_type.group_field.select_group != "none"
            -g '$plot_type.group_field.in_text'
        #end if

        $plot_type.label_location

    #end if

    ## General Plot Parameters ##
    #############################

    #if $plot_parameters.figure_height
    --height '$plot_parameters.figure_height'
    #end if

    #if $plot_parameters.figure_width
    --width '$plot_parameters.figure_width'
    #end if

    #if $plot_parameters.tick_width
    --tick-width '$plot_parameters.tick_width'
    #end if

    #if $plot_parameters.title
    --title '$plot_parameters.title'
    #end if

    #if $plot_parameters.x_label
    --xlab '$plot_parameters.x_label'
    #end if

    #if $plot_parameters.min_x
    --x-min '$plot_parameters.min_x'
    #end if

    #if $plot_parameters.max_x
    --x-max '$plot_parameters.max_x'
    #end if

    #if $plot_parameters.y_label
    --ylab '$plot_parameters.y_label'
    #end if

    #if $plot_parameters.min_y
    --y-min '$plot_parameters.min_y'
    #end if

    #if $plot_parameters.max_y
    --y-max '$plot_parameters.max_y'
    #end if
    
    ## To output ##
    ###############
    > plot.png

    ]]></command>
    <inputs>
        <expand macro="singular_input"/>
        <conditional name="plot_type">
            <param name="plot" type="select" label="Select plot type">
                <option value="histogram">Histogram</option>
                <option value="boxplot">Boxplot</option>
                <option value="line">Line/Scatter</option>
            </param>
            <when value="histogram">
                <expand macro="plot_field" />
                <param name="colour" type="integer"
                    min="1" max="7"
                    value="1"
                    argument="--color-index"
                    label="Select colour scheme"
                    help="Choose a number from 1-7"
                />
            </when>
            <when value="boxplot" >
                <expand macro="plot_field" />
                <expand macro="groups_input" />
                <param type="boolean" name="horizontal" label="Horizontal Box Plot" argument="--horiz"
                    checked="false"
                    falsevalue=""
                    truevalue="--horiz"
                />
                <param name="box_width" type="float"
                    label="Box Width (Optional)"
                    argument="--box-width"
                    optional="true"
                />
            </when>
            <when value="line">
                <param name="scatter" type="boolean" label="Scatter Plot" argument="--scatter"
                    checked="false"
                    falsevalue=""
                    truevalue="--scatter"
                    help="Plot only points, no lines"
                />
                <conditional name="column_text" >
                    <param type="select" name="select" label="Select input data columns for the X and Y axis based on:" >
                        <option value="string">Column Name</option>
                        <option value="column">Column Number</option>
                    </param>
                    <when value="column">
                        <param type="data_column" name="in_text_x"
                            data_ref="in_1"
                            multiple="false"
                            label="X-axis data column"
                        />
                        <param type="data_column" name="in_text_y"
                            data_ref="in_1"
                            multiple="false"
                            label="Y-axis data column"
                        />
                    </when>
                    <when value="string">
                        <param type="text" name="in_text_x"
                            optional="false"
                            label="X-axis data column"
                            help="Can use column name or column number">
                            <expand macro="text_sanitizer" />
                        </param>
                        <param type="text" name="in_text_y"
                            optional="false"
                            label="Y-axis data column"
                            help="Can use column name or column number">
                        </param>
                    </when>
                </conditional>
                <expand macro="groups_input" />
                <param name="label_location" type="select" label="Label Location"
                    help="Only displays legend if a groups column is set">
                    <option value="--legend-left">Left edge of plot</option>
                    <option value="--legend-top">Top edge of plot</option>
                </param>
            </when>
        </conditional>
        <expand macro="global_plot_parameters" />
        <expand macro="global_parameters" />
    </inputs>
    <outputs>
        <data format="png" from_work_dir="plot.png" name="out_plot" label="${in_1.name} ${plot_type.plot}" />
    </outputs>
    <tests>
        <test>
            <param name="in_1" value="plot.csv" />
            <conditional name="plot_type">
                <param name="plot" value="histogram" />
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="2" />
                </conditional>
                <param name="colour" value="2" />
            </conditional>
            <output name="out_plot" value="plot.png" ftype="png" compare="sim_size" delta="20000" />
        </test>
        <test>
            <param name="in_1" value="plot.csv" />
            <conditional name="plot_type">
                <param name="plot" value="boxplot" />
                <conditional name="column_text">
                    <param name="select" value="column" />
                    <param name="in_text" value="2" />
                </conditional>
                <conditional name="group_field">
                    <param name="select_group" value="string" />
                    <param name="in_text" value="1" />
                </conditional>
                <param name="horizontal" value="true" />
                <param name="box_width" value="50.5" />
            </conditional>
            <output name="out_plot" value="plot_box.png" compare="sim_size" delta="20000" />
        </test>
        <test>
            <param name="in_1" value="plot.csv" />
            <conditional name="plot_type">
                <param name="plot" value="line" />
                <param name="scatter" value="true" />
                <conditional name="column_text">
                    <param name="select" value="column" />
                    <param name="in_text_x" value="2" />
                    <param name="in_text_y" value="3" />
                </conditional>
                <conditional name="group_field">
                    <param name="select_group" value="string" />
                    <param name="in_text" value="1" />
                </conditional>
            </conditional>
            <output name="out_plot" value="plot_scatter.png" compare="sim_size" delta="20000" />
        </test>
        <test>
            <param name="in_1" value="plot.csv" />
            <conditional name="plot_type">
                <param name="plot" value="line" />
                <param name="scatter" value="false" />
                <conditional name="column_text">
                    <param name="select" value="column" />
                    <param name="in_text_x" value="2" />
                    <param name="in_text_y" value="3" />
                </conditional>
                <conditional name="group_field">
                    <param name="select_group" value="string" />
                    <param name="in_text" value="1" />
                </conditional>
                <param name="label_location" value="--legend-top" />
            </conditional>
            <section name="plot_parameters">
                <param name="figure_height" value="10.1" />
                <param name="figure_width" value="6.6" />
                <param name="tick_width" value="2.1" />
                <param name="title" value="Test" />
                <param name="x_label" value="Potentially Broken" />
                <param name="min_x" value="1.1" />
                <param name="max_x" value="109.1" />
                <param name="y_label" value="How High Can We Go?" />
                <param name="min_y" value="-10.4" />
                <param name="max_y" value="141.9" />
            </section>
            <output name="out_plot" value="line_all_param.png" compare="sim_size" delta="20000" />
        </test>
    </tests>
    <help><![CDATA[
    
Csvtk - Plot Help
-----------------

Info
####

Use Csvtk-Plot to plot histograms, line plots / scatter plots, or boxplots. 

Specify a column or a couple of columns from an input CSV/TSV dataset to generate wanted plots fast.

.. class:: warningmark

    Single quotes are not allowed in text inputs!

@HELP_INPUT_DATA@


@HELP_END_STATEMENT@


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