annotate macros.xml @ 4:c237ba772225 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"

<macros>
    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
    <token name="@WRAPPER_VERSION@">3.1.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement>
            <!--<requirement type="package" version="3.7">python</requirement>-->
            <yield />
        </requirements>
        <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.5281/zenodo.1133705</citation>
            <yield />
        </citations>
    </xml>

    <xml name="colormap">
        <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
            <option value="RdYlBu">RdYlBu</option>
            <option value="Accent">Accent</option>
            <option value="Spectral">Spectral</option>
            <option value="Set1">Set1</option>
            <option value="Set2">Set2</option>
            <option value="Set3">Set3</option>
            <option value="Dark2">Dark2</option>
            <option value="Reds">Reds</option>
            <option value="Oranges">Oranges</option>
            <option value="Greens">Greens</option>
            <option value="Blues">Blues</option>
            <option value="Greys">Greys</option>
            <option value="Purples">Purples</option>
            <option value="Paired">Paired</option>
            <option value="Pastel1">Pastel1</option>
            <option value="Pastel2">Pastel2</option>
            <option value="spring">spring</option>
            <option value="summer">summer</option>
            <option value="autumn">autumn</option>
            <option value="winter">winter</option>
            <option value="hot">hot</option>
            <option value="coolwarm">coolwarm</option>
            <option value="cool">cool</option>
            <option value="seismic">seismic</option>
            <option value="terrain">terrain</option>
            <option value="ocean">ocean</option>
            <option value="rainbow">rainbow</option>
            <option value="bone">bone</option>
            <option value="flag">flag</option>
            <option value="prism">prism</option>
            <option value="cubehelix">cubehelix</option>
            <option value="binary">binary</option>
            <option value="pink">pink</option>
            <option value="gray">gray</option>
            <option value="copper">copper</option>
            <option value="BrBG">BrBG</option>
            <option value="BuGn">BuGn</option>
            <option value="BuPu">BuPu</option>
            <option value="GnBu">GnBu</option>
            <option value="OrRd">OrRd</option>
            <option value="PiYG">PiYG</option>
            <option value="PRGn">PRGn</option>
            <option value="PuOr">PuOr</option>
            <option value="PuRd">PuRd</option>
            <option value="PuBu">PuBu</option>
            <option value="RdBu">RdBu</option>
            <option value="RdGy">RdGy</option>
            <option value="RdPu">RdPu</option>
            <option value="YlGn">YlGn</option>
            <option value="PuBuGn">PuBuGn</option>
            <option value="RdYlGn">RdYlGn</option>
            <option value="YlGnBu">YlGnBu</option>
            <option value="YlOrBr">YlOrBr</option>
            <option value="YlOrRd">YlOrRd</option>
            <option value="gist_gray">gist_gray</option>
            <option value="gist_stern">gist_stern</option>
            <option value="gist_earth">gist_earth</option>
            <option value="gist_yarg">gist_yarg</option>
            <option value="gist_ncar">gist_ncar</option>
            <option value="gist_rainbow">gist_rainbow</option>
            <option value="gist_heat">gist_heat</option>
            <option value="gnuplot">gnuplot</option>
            <option value="gnuplot2">gnuplot2</option>
            <option value="CMRmap">CMRmap</option>
            <option value="bwr">bwr</option>
            <option value="hsv">hsv</option>
            <option value="brg">brg</option>
            <option value="jet">jet</option>
            <option value="afmhot">afmhot</option>
            <option value="Accent_r">Accent reversed</option>
            <option value="Spectral_r">Spectral reversed</option>
            <option value="Set1_r">Set1 reversed</option>
            <option value="Set2_r">Set2 reversed</option>
            <option value="Set3_r">Set3 reversed</option>
            <option value="Dark2_r">Dark2 reversed</option>
            <option value="Reds_r">Reds reversed</option>
            <option value="Oranges_r">Oranges reversed</option>
            <option value="Greens_r">Greens reversed</option>
            <option value="Blues_r">Blues reversed</option>
            <option value="Greys_r">Greys reversed</option>
            <option value="Purples_r">Purples reversed</option>
            <option value="Paired_r">Paired reversed</option>
            <option value="Pastel1_r">Pastel1 reversed</option>
            <option value="Pastel2_r">Pastel2 reversed</option>
            <option value="spring_r">spring reversed</option>
            <option value="summer_r">summer reversed</option>
            <option value="autumn_r">autumn reversed</option>
            <option value="winter_r">winter reversed</option>
            <option value="hot_r">hot reversed</option>
            <option value="coolwarm_r">coolwarm reversed</option>
            <option value="cool_r">cool reversed</option>
            <option value="seismic_r">seismic reversed</option>
            <option value="terrain_r">terrain reversed</option>
            <option value="ocean_r">ocean reversed</option>
            <option value="rainbow_r">rainbow reversed</option>
            <option value="bone_r">bone reversed</option>
            <option value="flag_r">flag reversed</option>
            <option value="prism_r">prism reversed</option>
            <option value="cubehelix_r">cubehelix reversed</option>
            <option value="binary_r">binary reversed</option>
            <option value="pink_r">pink reversed</option>
            <option value="gray_r">gray reversed</option>
            <option value="copper_r">copper reversed</option>
            <option value="BrBG_r">BrBG reversed</option>
            <option value="BuGn_r">BuGn reversed</option>
            <option value="BuPu_r">BuPu reversed</option>
            <option value="GnBu_r">GnBu reversed</option>
            <option value="OrRd_r">OrRd reversed</option>
            <option value="PiYG_r">PiYG reversed</option>
            <option value="PRGn_r">PRGn reversed</option>
            <option value="PuOr_r">PuOr reversed</option>
            <option value="PuRd_r">PuRd reversed</option>
            <option value="PuBu_r">PuBu reversed</option>
            <option value="RdBu_r">RdBu reversed</option>
            <option value="RdGy_r">RdGy reversed</option>
            <option value="RdPu_r">RdPu reversed</option>
            <option value="YlGn_r">YlGn reversed</option>
            <option value="PuBuGn_r">PuBuGn reversed</option>
            <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
            <option value="RdYlGn_r">RdYlGn reversed</option>
            <option value="YlGnBu_r">YlGnBu reversed</option>
            <option value="YlOrBr_r">YlOrBr reversed</option>
            <option value="YlOrRd_r">YlOrRd reversed</option>
            <option value="gist_gray_r">gist_gray reversed</option>
            <option value="gist_stern_r">gist_stern reversed</option>
            <option value="gist_earth_r">gist_earth reversed</option>
            <option value="gist_yarg_r">gist_yarg reversed</option>
            <option value="gist_ncar_r">gist_ncar reversed</option>
            <option value="gist_rainbow_r">gist_rainbow reversed</option>
            <option value="gist_heat_r">gist_heat reversed</option>
            <option value="gnuplot_r">gnuplot reversed</option>
            <option value="gnuplot2_r">gnuplot2 reversed</option>
            <option value="CMRmap_r">CMRmap reversed</option>
            <option value="bwr_r">bwr reversed</option>
            <option value="hsv_r">hsv reversed</option>
            <option value="brg_r">brg reversed</option>
            <option value="jet_r">jet reversed</option>
            <option value="afmhot_r">afmhot reversed</option>
        </param>
    </xml>

    <xml name="region">
        <param argument="--region" type="text" label="Region of the genome to limit the operation"
            help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />
    </xml>

    <xml name='matrix_h5_cooler_multiple_macro'>
        <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
            label="Matricies to compute on" multiple="true"/>
    </xml>
    <token name="@REFERENCES@">

.. class:: infomark

For more information on the tools, please visit our `help site`_.

If you would like to give us feedback or you run into any trouble, please send an email to [e-mail]

This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for
Immunobiology and Epigenetics`_.

.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _help site: https://github.com/deeptools/pyGenomeTracks

    </token>

    <xml name="track_input_bed_macro">
        <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple='True'/>
    </xml>
    <xml name="track_input_bed_gtf_macro">
        <param name="track_input_bed" type="data" format="bed,gtf" label="Track file bed or gtf format" multiple='True'/>
    </xml>
    <xml name="track_input_narrow_peak_macro">
        <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file encodepeak or format" multiple='True'/>
    </xml>
    <xml name="track_input_bed_single_macro">
        <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/>
    </xml>
    <xml name="track_input_bedgraph_macro">
        <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" multiple='True'/>
    </xml>
    <xml name="track_input_bigwig_macro">
        <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" multiple='True'/>
    </xml>
    <xml name="track_input_bedgraph_matrix_macro">
        <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" multiple='True'/>
    </xml>
    <xml name="plot_title">
        <param name="title" type="text" optional="true" label="Plot title" multiple='True'/>
    </xml>
    <xml name="spacer_macro">
        <param name="spacer_height" type="float" value="" optional="True"
              label="Include spacer at the end of the track" help="Height of the spacer." />
    </xml>
    <xml name="inverted_macro">
        <param name="invert_orientation" type="boolean" truevalue="yes" falsevalue="no" checked="false"
               label="Invert the track" />
    </xml>
    <xml name="color_bed_macro">
        <conditional name="color_bed">
            <param name="color_bed_select" type="select" label="Use color:">
                <option value="manually" selected="True">manually</option>
                <option value="bed_rgb">From the 9th field</option>
                <option value="colormap">From the 5th field (score)</option>
            </param>
            <when value="manually">
                <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
            </when>
            <when value="bed_rgb" />
            <when value="colormap">
              <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
                <option value="RdYlBu">RdYlBu</option>
                <option value="Accent">Accent</option>
                <option value="Spectral">Spectral</option>
                <option value="Set1">Set1</option>
                <option value="Set2">Set2</option>
                <option value="Set3">Set3</option>
                <option value="Dark2">Dark2</option>
                <option value="Reds">Reds</option>
                <option value="Oranges">Oranges</option>
                <option value="Greens">Greens</option>
                <option value="Blues">Blues</option>
                <option value="Greys">Greys</option>
                <option value="Purples">Purples</option>
                <option value="Paired">Paired</option>
                <option value="Pastel1">Pastel1</option>
                <option value="Pastel2">Pastel2</option>
                <option value="spring">spring</option>
                <option value="summer">summer</option>
                <option value="autumn">autumn</option>
                <option value="winter">winter</option>
                <option value="hot">hot</option>
                <option value="coolwarm">coolwarm</option>
                <option value="cool">cool</option>
                <option value="seismic">seismic</option>
                <option value="terrain">terrain</option>
                <option value="ocean">ocean</option>
                <option value="rainbow">rainbow</option>
                <option value="bone">bone</option>
                <option value="flag">flag</option>
                <option value="prism">prism</option>
                <option value="cubehelix">cubehelix</option>
                <option value="binary">binary</option>
                <option value="pink">pink</option>
                <option value="gray">gray</option>
                <option value="copper">copper</option>
                <option value="BrBG">BrBG</option>
                <option value="BuGn">BuGn</option>
                <option value="BuPu">BuPu</option>
                <option value="GnBu">GnBu</option>
                <option value="OrRd">OrRd</option>
                <option value="PiYG">PiYG</option>
                <option value="PRGn">PRGn</option>
                <option value="PuOr">PuOr</option>
                <option value="PuRd">PuRd</option>
                <option value="PuBu">PuBu</option>
                <option value="RdBu">RdBu</option>
                <option value="RdGy">RdGy</option>
                <option value="RdPu">RdPu</option>
                <option value="YlGn">YlGn</option>
                <option value="PuBuGn">PuBuGn</option>
                <option value="RdYlGn">RdYlGn</option>
                <option value="YlGnBu">YlGnBu</option>
                <option value="YlOrBr">YlOrBr</option>
                <option value="YlOrRd">YlOrRd</option>
                <option value="gist_gray">gist_gray</option>
                <option value="gist_stern">gist_stern</option>
                <option value="gist_earth">gist_earth</option>
                <option value="gist_yarg">gist_yarg</option>
                <option value="gist_ncar">gist_ncar</option>
                <option value="gist_rainbow">gist_rainbow</option>
                <option value="gist_heat">gist_heat</option>
                <option value="gnuplot">gnuplot</option>
                <option value="gnuplot2">gnuplot2</option>
                <option value="CMRmap">CMRmap</option>
                <option value="bwr">bwr</option>
                <option value="hsv">hsv</option>
                <option value="brg">brg</option>
                <option value="jet">jet</option>
                <option value="afmhot">afmhot</option>
                <option value="Accent_r">Accent reversed</option>
                <option value="Spectral_r">Spectral reversed</option>
                <option value="Set1_r">Set1 reversed</option>
                <option value="Set2_r">Set2 reversed</option>
                <option value="Set3_r">Set3 reversed</option>
                <option value="Dark2_r">Dark2 reversed</option>
                <option value="Reds_r">Reds reversed</option>
                <option value="Oranges_r">Oranges reversed</option>
                <option value="Greens_r">Greens reversed</option>
                <option value="Blues_r">Blues reversed</option>
                <option value="Greys_r">Greys reversed</option>
                <option value="Purples_r">Purples reversed</option>
                <option value="Paired_r">Paired reversed</option>
                <option value="Pastel1_r">Pastel1 reversed</option>
                <option value="Pastel2_r">Pastel2 reversed</option>
                <option value="spring_r">spring reversed</option>
                <option value="summer_r">summer reversed</option>
                <option value="autumn_r">autumn reversed</option>
                <option value="winter_r">winter reversed</option>
                <option value="hot_r">hot reversed</option>
                <option value="coolwarm_r">coolwarm reversed</option>
                <option value="cool_r">cool reversed</option>
                <option value="seismic_r">seismic reversed</option>
                <option value="terrain_r">terrain reversed</option>
                <option value="ocean_r">ocean reversed</option>
                <option value="rainbow_r">rainbow reversed</option>
                <option value="bone_r">bone reversed</option>
                <option value="flag_r">flag reversed</option>
                <option value="prism_r">prism reversed</option>
                <option value="cubehelix_r">cubehelix reversed</option>
                <option value="binary_r">binary reversed</option>
                <option value="pink_r">pink reversed</option>
                <option value="gray_r">gray reversed</option>
                <option value="copper_r">copper reversed</option>
                <option value="BrBG_r">BrBG reversed</option>
                <option value="BuGn_r">BuGn reversed</option>
                <option value="BuPu_r">BuPu reversed</option>
                <option value="GnBu_r">GnBu reversed</option>
                <option value="OrRd_r">OrRd reversed</option>
                <option value="PiYG_r">PiYG reversed</option>
                <option value="PRGn_r">PRGn reversed</option>
                <option value="PuOr_r">PuOr reversed</option>
                <option value="PuRd_r">PuRd reversed</option>
                <option value="PuBu_r">PuBu reversed</option>
                <option value="RdBu_r">RdBu reversed</option>
                <option value="RdGy_r">RdGy reversed</option>
                <option value="RdPu_r">RdPu reversed</option>
                <option value="YlGn_r">YlGn reversed</option>
                <option value="PuBuGn_r">PuBuGn reversed</option>
                <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
                <option value="RdYlGn_r">RdYlGn reversed</option>
                <option value="YlGnBu_r">YlGnBu reversed</option>
                <option value="YlOrBr_r">YlOrBr reversed</option>
                <option value="YlOrRd_r">YlOrRd reversed</option>
                <option value="gist_gray_r">gist_gray reversed</option>
                <option value="gist_stern_r">gist_stern reversed</option>
                <option value="gist_earth_r">gist_earth reversed</option>
                <option value="gist_yarg_r">gist_yarg reversed</option>
                <option value="gist_ncar_r">gist_ncar reversed</option>
                <option value="gist_rainbow_r">gist_rainbow reversed</option>
                <option value="gist_heat_r">gist_heat reversed</option>
                <option value="gnuplot_r">gnuplot reversed</option>
                <option value="gnuplot2_r">gnuplot2 reversed</option>
                <option value="CMRmap_r">CMRmap reversed</option>
                <option value="bwr_r">bwr reversed</option>
                <option value="hsv_r">hsv reversed</option>
                <option value="brg_r">brg reversed</option>
                <option value="jet_r">jet reversed</option>
                <option value="afmhot_r">afmhot reversed</option>
              </param>
            </when>
        </conditional>
        <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
    </xml>
    <xml name="color_coverage_macro">
        <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
        <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
        <conditional name="color_negative">
            <param name="color_negative_select" type="select" label="Use a different color for negative values">
                <option value="no" selected="True">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="color" type="color" value="#000000" label="Color of negative values" optional="True" />
            </when>
        </conditional>
    </xml>
    <xml name="overlay_macro">
        <param name="overlay_select" type="select" label="Overlay this track with the previous one:">
            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
            <option value="share-y">Yes and keep same y axis</option>
        </param>
    </xml>
    <xml name="type_coverage_macro">
        <conditional name="type_conditional">
            <param name="type_selector" type="select" label="Choose style of the plot.">
                <option value="fill_option">fill</option>
                <option value="line_option">line</option>
                <option value="point_option">point</option>
            </param>
            <when value="line_option">
                <param name="width_line" type="float" value="0.5" optional="True" label="Width"/>
            </when>
            <when value="point_option">
                <param name="width_point" type="float" value="0.5" optional="True" label="Width"/>
            </when>
            <when value="fill_option" />
        </conditional>
    </xml>
    <xml name="minmax_macro">
        <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
        <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
    </xml>
    <xml name="reading_bw_macro">
        <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False">
            <param name="summary" type="select" label="Summary method">
                <option value="mean" selected="True">mean=mean value</option>
                <option value="min">min=minimum value</option>
                <option value="max">max=maximum value</option>
                <option value="coverage">coverage=number of covered bases</option>
                <option value="std">std=standard deviation</option>
            </param>
            <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
            <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false"
                   label="NAN's to zeros" />
        </section>
    </xml>
</macros>