comparison macros.xml @ 3:5186eda61ca4 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5

2:cdff00acac0f

<macros>
    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
    <token name="@WRAPPER_VERSION@">1.8.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
            <yield />
        </requirements>
        <version_command>@BINARY@ --version</version_command>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.5281/zenodo.159780</citation>
            <yield />
        </citations>
    </xml>

    <xml name="zMax">

    </xml>


    <xml name="multiple_input_matrices">
        <repeat name="input_files" title="HiC Matrix files" min="2">
            <param name="matrix" type="data" format="h5"
                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."/>

    <token name="@multiple_input_matrices@">
        #set $matrices = []
        #set $mlabels = []
        #for $counter, $i in enumerate($input_files):
            ln -s $i.matrix #echo str($counter)+'.npz.h5'#;
            #silent $matrices.append( '%s.npz.h5' % $counter )

            #if str($i.mlabel.value) != "":
                #set $mlabels += ['"%s"' % ($i.mlabel.value)]
            #else
                #set $mlabels += ['"%s"' % ($i.matrix.name)]

    <xml name="pseudocount">
        <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
    </xml>

    <token name="@REFERENCES@">

.. class:: infomark

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

            </filter>
        </data>
    </xml>

    <xml name="track_input_h5_macro">
        <param name="track_input_h5" type="data" format="h5" label="Track file h5 format"/>
    </xml>
    <xml name="track_input_bed_macro">
        <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
    </xml>
    <xml name="track_input_bedgraph_macro">

3:5186eda61ca4

<macros>
    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
    <token name="@WRAPPER_VERSION@">2.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
            <yield />
        </requirements>
        <version_command>@BINARY@ --version</version_command>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.5281/zenodo.1123667</citation>
            <yield />
        </citations>
    </xml>

    <xml name="zMax">

    </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."/>

    <token name="@multiple_input_matrices@">
        #set $matrices = []
        #set $mlabels = []
        #for $counter, $i in enumerate($input_files):
            ln -s $i.matrix #echo str($counter)+'_matrix'#;
            #silent $matrices.append( '%s_matrix' % $counter )

            #if str($i.mlabel.value) != "":
                #set $mlabels += ['"%s"' % ($i.mlabel.value)]
            #else
                #set $mlabels += ['"%s"' % ($i.matrix.name)]

    <xml name="pseudocount">
        <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
    </xml>
    <xml name='matrix_h5_cooler_macro'>
    <param name='matrix_h5_cooler'  type="data" format="h5,cool" 
                            label="Matrix to compute on."/>
       
    </xml>
    <xml name='matrix_h5_cooler_multiple_macro'>
        <param name='matrix_h5_cooler_multiple'  type="data" format="h5,cool" 
                            label="Matrix to compute on." multiple="True"/>
    </xml>
    <token name="@REFERENCES@">

.. class:: infomark

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

            </filter>
        </data>
    </xml>

    <xml name="track_input_h5_macro">
        <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
    </xml>
    <xml name="track_input_bed_macro">
        <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
    </xml>
    <xml name="track_input_bedgraph_macro">