comparison macros.xml @ 8:b05f292d220c draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8

7:43332e51a712

<macros>
    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
    <token name="@WRAPPER_VERSION@">2.1</token>

    <token name="@USE_RANGE@">
        #if $use_range.select_use_range == "yes_use_range":
            --range $range_min:$range_max
        #end if
    </token>

    <xml name="zMax">
        <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
    </xml>
    <xml name="use_range">
        <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
            <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
                <option value="no_use_range">No restriction</option>
                <option value="yes_use_range">Only consider counts within a range</option>
            </param>
            <when value="no_use_range"/>
            <when value="yes_use_range">

            </when>
        </conditional>
    </xml>

    <xml name="range">
        <param name="range_min" type="integer" value="" min="0"/>
        <param name="range_max" type="integer" value="" min="0"/>
    </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>

        </param>
    </xml>


    <xml name="multiple_input_matrices">
        <repeat name="input_files" title="HiC Matrix files" min="2">
            <param name="matrix" type="data" format="h5,cool"
                label="HiC Matrix file"
                help=""/>
            <param name="mlabel" type="text" size="30" optional="true" value=""
                label="Label"
                help="Label to use in the output. If not given the dataset name will be used instead."/>
        </repeat>

8:b05f292d220c

<macros>
    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
    <token name="@WRAPPER_VERSION@">2.1.2</token>
    <token name="@USE_RANGE@">
        #if $use_range.select_use_range == "yes_use_range":
            --range $range_min:$range_max
        #end if
    </token>

    <xml name="zMax">
        <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
    </xml>
    <xml name="use_range">
        <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
            <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">
                <option value="no_use_range">No restriction</option>
                <option value="yes_use_range">Only consider counts within a range</option>
            </param>
            <when value="no_use_range"/>
            <when value="yes_use_range">

            </when>
        </conditional>
    </xml>

    <xml name="range">
        <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>
        <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
    </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>

        </param>
    </xml>


    <xml name="multiple_input_matrices">
        <repeat name="input_files" title="Hi-C Matrix files" min="2">
            <param name="matrix" type="data" format="h5,cool"
                label="Hi-C Matrix file"
                help=""/>
            <param name="mlabel" type="text" size="30" optional="true" value=""
                label="Label"
                help="Label to use in the output. If not given the dataset name will be used instead."/>
        </repeat>