annotate macros.xml @ 15:36b848d5f3ec draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 7df009cda0bc57c6891fc5273b2440db6fcf5719

<macros>
    <token name="@TOOL_VERSION@">3.8</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">pygenometracks</requirement>
            <yield />
        </requirements>
        <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command>
    </xml>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">pygenometracks</xref>
        </xrefs>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/s41467-017-02525-w</citation>
            <citation type="doi">10.1093/bioinformatics/btaa692</citation>
            <yield />
        </citations>
    </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>
    <!-- all input files-->
    <xml name="matrix_h5_cooler_multiple_macro">
        <param name="matrix_h5_cooler_multiple" type="data" format="h5,cool"
            label="Matricies to plot" multiple="true"/>
    </xml>
    <xml name="track_input_bed_macro">
        <param name="track_input_bed" type="data" format="bed" label="Track file(s) 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(s) 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(s) encodepeak or bed 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(s) bedgraph format" multiple="True"/>
    </xml>
    <xml name="track_input_bigwig_macro">
        <param name="track_input_bigwig" type="data" format="bigwig" label="Track file(s) 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(s) bedgraph format" multiple="True"/>
    </xml>
    <xml name="track_input_link_macro">
        <param name="track_input_link" type="data" format="bed,interval" label="Track file(s) for links" multiple="True"/>
    </xml>
    <xml name="track_input_fasta_macro">
        <conditional name="fasta_source">
            <param name="fasta_source_selector" type="select" label="Choose the source for the fasta to display">
                <option value="cached">Locally cached</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param name="fasta_cached" type="select" label="Fasta availables">
                    <options from_data_table="fasta_indexes">
                        <validator type="no_options" message="No cached fasta is available"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="fasta_local" type="data" format="fasta" label="Fasta from history"/>
            </when>
        </conditional>
    </xml>
    <xml name="track_input_maf_macro">
        <param name="track_input_maf" type="data" format="maf" label="Track file for maf" multiple="False"/>
    </xml>
    <!-- Common to nearly all tracks: -->
    <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="true" falsevalue="false" checked="false"
               label="Invert the track" />
    </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="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>
    <!-- More specific but still present twice:-->
    <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="false" selected="True">No</option>
                <option value="true">Yes</option>
            </param>
            <when value="false" />
            <when value="true">
                <param name="color" type="color" value="#000000" label="Color of negative values" optional="True" />
            </when>
        </conditional>
    </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="logScale_coverage_macro">
        <conditional name="logScale_conditional">
            <param name="transform_selector" type="select" label="Choose a transformation">
                <option value="no">no transformation</option>
                <option value="log1p">log1p</option>
                <option value="log">log</option>
                <option value="log2">log2</option>
                <option value="log10">log10</option>
                <option value="-log">-log</option>
            </param>
            <when value="no"/>
            <when value="log1p">
                <param name="y_axis_values" type="boolean" truevalue="original" falsevalue="transformed" checked="false"
                label="Use original values instead of transformed values." />
            </when>
            <when value="log">
                <param name="log_pseudocount" type="float"  value="0" label="pseudo count to add before applying log" />
                <param name="y_axis_values" type="boolean" truevalue="original" falsevalue="transformed" checked="false"
                label="Use original values instead of transformed values." />
            </when>
            <when value="log2">
                <param name="log_pseudocount" type="float"  value="0" label="pseudo count to add before applying log2" />
                <param name="y_axis_values" type="boolean" truevalue="original" falsevalue="transformed" checked="false"
                label="Use original values instead of transformed values." />
            </when>
            <when value="log10">
                <param name="log_pseudocount" type="float"  value="0" label="pseudo count to add before applying log10" />
                <param name="y_axis_values" type="boolean" truevalue="original" falsevalue="transformed" checked="false"
                label="Use original values instead of transformed values." />
            </when>
            <when value="-log">
                <param name="log_pseudocount" type="float"  value="0" label="pseudo count to add before applying -log" />
                <param name="y_axis_values" type="boolean" truevalue="original" falsevalue="transformed" checked="false"
                label="Use original values instead of transformed values." />
            </when>
        </conditional>
    </xml>
    <xml name="border_color_bed_macro">
        <conditional name="border_color_bed">
            <param name="border_color_bed_select" type="select" label="Define border color:">
                <option value="manually" selected="True">manually</option>
                <option value="bed_rgb">From the 9th field</option>
                <option value="none">No border</option>
            </param>
            <when value="manually">
                <param name="color" type="color" value="#000000" label="Color of the border"/>
            </when>
            <when value="bed_rgb" />
            <when value="none" />
        </conditional>
    </xml>
    <xml name="backbone_color_bed_macro">
        <conditional name="backbone_color_bed">
            <param name="backbone_color_bed_select" type="select" label="Define the color of the backbone:">
                <option value="manually" selected="True">manually</option>
                <option value="bed_rgb">From the 9th field</option>
                <option value="none">No border</option>
            </param>
            <when value="manually">
                <param name="color" type="color" value="#000000" label="Color of the backbone"/>
            </when>
            <when value="bed_rgb" />
            <when value="none" />
        </conditional>
    </xml>
    <xml name="bed_advanced_macro">
        <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false"
                label="Global max rows" />
        <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" />
        <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" />
        <param name="line_width" type="float" value="0.5" label="width of lines" />
        <section name ="gtf" title="When using gtf as input" expanded="False">
            <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label"
                help="Usually transcript_name or gene_name"/>
            <conditional name="merge_transcripts">
                <param name="merge_transcripts_select" type="select" label="Merge all transcripts of each gene in a single entry">
                    <option value="false" selected="True">No</option>
                    <option value="true">Yes</option>
                </param>
                <when value="true">
                    <param name="merge_overlapping_exons" type="boolean" truevalue="true" falsevalue="false" checked="true"
                        label="Merge overlapping exons" help="Usually it makes prettier plots" />
                </when>
                <when value="false" />
            </conditional>
        </section>
    </xml>
    <xml name="utr_macro">
        <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions"/>
        <conditional name="color_utr">
            <param name="color_utr_select" type="select" label="Define UTR color:">
                <option value="manually" selected="True">manually</option>
                <option value="bed_rgb">From the 9th field</option>
                <option value="like">Like the coding</option>
            </param>
            <when value="manually">
                <param name="color" type="color" value="grey" label="Color of UTR regions"/>
            </when>
            <when value="bed_rgb" />
            <when value="like" />
        </conditional>
    </xml>
    <xml name="lines_macro">
        <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"/>
        <param name="line_width" type="float" value="0.5" label="width of line(s)" optional="True"/>
        <param name="line_style" type="select" label="Style of the line(s)">
            <option value="solid" selected="True">Solid</option>
            <option value="dashed">Dashed</option>
            <option value="dotted">Dotted</option>
            <option value="dashdot">Dashdot</option>
        </param>
    </xml>
    <xml name="colormap_macro_noRdYlBu_r_noViridis">
        <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="plasma">plasma</option>
        <option value="inferno">inferno</option>
        <option value="magma">magma</option>
        <option value="cividis">cividis</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="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>
        <option value="viridis_r">viridis reversed</option>
        <option value="plasma_r">plasma reversed</option>
        <option value="inferno_r">inferno reversed</option>
        <option value="magma_r">magma reversed</option>
        <option value="cividis_r">cividis reversed</option>
    </xml>
    <xml name="links_arcs_triangles_options">
        <param name="compact_arcs_level" type="select" label="Height of arcs and triangles:">
            <option value="0" selected="True">default (proportional to distance)</option>
            <option value="1">compacted (the height is proportional to the square root of the distance)</option>
            <option value="2">highly compacted (the height is the same for all distances)</option>
        </param>
        <param name="use_middle" type="select" label="Coordinates to use" help="Not useful with loops">
            <option value="false" selected="True">Extremities (start of first and end of second)</option>
            <option value="true">Center (mean of start and end for each)</option>
        </param>
    </xml>
    <xml name="region2_option">
        <param name="region2" type="text" label="Region of the genome that should be plotted on the y axis" optional="true"
            value="" help="The format is chr:start-end, for example chr10:10-500. By default this is the region on the x-axis. Top is start and bottom is end. Use 'Invert the track' if you want the contrary.">
            <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator>
        </param>
    </xml>
</macros>