annotate paracords_plot.xml @ 2:9958188c6195 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit b26c6ec671ec63cce1f86c70e928673ed2c82f82"

<tool id="plotly_parallel_coordinates_plot" name="Parallel Coordinates Plot" version="0.2">
    <description>of tabular data</description>
    <requirements>
        <requirement type="package" version="3.6">python</requirement>
        <requirement type="package" version="0.22.0">pandas</requirement>
        <requirement type="package" version="3.1.1">plotly</requirement>
    </requirements>
    <version_command>echo $version</version_command>
    <command detect_errors="aggressive"><![CDATA[
    python '$__tool_directory__/paracords_plot.py'
        -i '$infile'
        -m '$dimension_selections.selected_mode'
        -d '$dimension_selections.col_dimensions'
        -t '$categorized_datatype'
        -c '$col_color'
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="tabular" label="Select table data file "/>
        <conditional name="dimension_selections">
            <param name="selected_mode" type="select" label="The mode of column selection">
                <option value="by_index" selected="true">By index</option>
                <option value="by_name">By column name</option>
            </param>
            <when value="by_index">
                <param name="col_dimensions" multiple="true" type="data_column" data_ref="infile" use_header_names="true" display="checkboxes" label="Select the columns for dimentions:"/>
            </when>
            <when value="by_name">
                <param name="col_dimensions" type="text" value="^param_.*" label="Type the column names" help="Two modes: 1) multiple names separated by comma, e.g. header1,header2, or 2) include `*` to initiate regular expression searches for every column name, for example, ^param_.* will retreive all the headers starting with param_. Note: no mix of the two is supported. Use default sanitizer: string.ascii_letters + string.digits + &quot; -=_.()/+*^,:?!&quot;)"/>
            </when>
        </conditional>
        <param name="categorized_datatype" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Cast all the dimensions into categorical datatype?"/>
        <param name="col_color" type="data_column" data_ref="infile" use_header_names="true" label="Select a column containg the values for coloring:" help="e.g. mean_test_score"/>
    </inputs>

    <outputs>
        <data name="output" format="html" from_work_dir="output.html" label="Plot visualization of tabular data on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="parcoords01.tabular" ftype="tabular"/>
            <param name="col_dimensions" value="4,5"/>
            <param name="categorized_datatype" value="false"/>
            <param name="col_color" value="3"/>
            <output name="output" file="parcoords_plot01.html" compare="sim_size"/>
        </test>
        <test>
            <param name="infile" value="parcoords02.tabular" ftype="tabular"/>
            <param name="col_dimensions" value="4,5"/>
            <param name="categorized_datatype" value="false"/>
            <param name="col_color" value="3"/>
            <output name="output" file="parcoords_plot02.html" compare="sim_size"/>
        </test>
        <test>
            <param name="infile" value="parcoords02.tabular" ftype="tabular"/>
            <param name="selected_mode" value="by_name"/>
            <param name="col_dimensions" value="param_*"/>
            <param name="categorized_datatype" value="false"/>
            <param name="col_color" value="3"/>
            <output name="output" file="parcoords_plot02.html" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**


Produce a `parallel coordinates plot <https://plot.ly/python/parallel-coordinates-plot/>`_ from a tabular file.
Multiple columns are chosen for dimensions and a single column for coloring. The plot is buried in a html file which
provides rich interactive features. Image can be saved in various format, such as 'png', 'svg', 'jpeg' and so on.


    ]]>
    </help>
    <citations>
         <citation type="bibtex">
          @online{plotly,
          author = {Plotly Technologies Inc.},
          title = {Collaborative data science},
          publisher = {Plotly Technologies Inc.},
          address = {Montreal, QC}, year = {2015},
          url = {https://plot.ly} }
        </citation>
    </citations>
</tool>