comparison macros.xml @ 24:0147ee498251 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788

23:ba2a39a88953

<macros>
    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
    <token name="@TOOL_VERSION@">3.6</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@USE_RANGE@">
        #if $use_range.select_use_range == "yes_use_range":
            --range $use_range.range_min:$use_range.range_max
        #end if
    </token>

        </repeat>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.5281/zenodo.1133705</citation>
            <yield />
        </citations>
    </xml>
    <xml name="dpi">
        <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />

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

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

        <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" multiple="true" label="Matricies to compute on" />
    </xml>
    <xml name='convertFormat_single_macro'>
        <conditional name="inputFormat_conditional">
            <param name="inputFormat_selector" type="select" label="Choose input file type">
                <option value="optionCool" selected="True">cool</option>
                <option value="optionH5">h5</option>
                <option value="optionHic">hic</option>
                <option value="optionHomer">Homer</option>
                <option value="optionHicpro">HiCPro</option>
            </param>
            <when value="optionCool">
                <expand macro='matrix_h5_cooler_macro' />
                <param name='correctionName' type='text' label='Correction factors column name' />
                <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />

            </when>
            <when value="optionHomer">
                <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' />
            </when>
            <when value="optionHicpro">
                <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' />
                <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' />
            </when>
        </conditional>
    </xml>

    <xml name='convertFormat_multiple_macro'>

            <param name="inputFormat_selector" type="select" label="Choose input file type">
                <option value="optionCool" selected="True">cool</option>
                <option value="optionH5">h5</option>
                <option value="optionHomer">Homer</option>
                <option value="optionHicpro">HiCPro</option>
            </param>
            <when value="optionCool">
                <expand macro='matrix_h5_cooler_multiple_macro' />
                <param name='correctionName' type='text' label='Correction factors column name' />
                <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />

                <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' />
            </when>
            <when value="optionHicpro">
                <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' />
                <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' />
            </when>
        </conditional>
    </xml>
    <xml name='convertFormat_single_output_macro'>
        <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->

            <param name="outputFormat_selector" type="select" label="Choose output file type">
                <option value="cool" selected="True">cool</option>
                <option value="h5">h5</option>
                <option value="homer">Homer</option>
                <option value="ginteractions">ginteractions</option>
            </param>
            <when value="cool">
                <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
                <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
            </when>
            <when value='h5' />
            <when value='homer' />
            <when value='ginteractions' />
        </conditional>
    </xml>
    <token name="@REFERENCES@">

.. class:: infomark

24:0147ee498251

<macros>
    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
    <token name="@TOOL_VERSION@">3.7.5</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">23.0</token>
    <token name="@USE_RANGE@">
        #if $use_range.select_use_range == "yes_use_range":
            --range $use_range.range_min:$use_range.range_max
        #end if
    </token>

        </repeat>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/nar/gkaa220</citation>
            <citation type="doi">10.1093/nar/gky504</citation>
            <yield />
        </citations>
    </xml>
    <xml name="dpi">
        <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />

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

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

        <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" multiple="true" label="Matricies to compute on" />
    </xml>

    <xml name='matrix_cooler_multiple_macro'>
        <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" />
    </xml>
    <xml name='convertFormat_single_macro'>
        <conditional name="inputFormat_conditional">
            <param name="inputFormat_selector" type="select" label="Choose input file type">
                <option value="optionCool" selected="True">cool</option>
                <option value="optionH5">h5</option>
                <option value="optionHic">hic</option>
                <option value="optionHomer">Homer</option>
                <option value="optionHicpro">HiCPro</option>
                <option value="option2Dtext">2D-text</option>

            </param>
            <when value="optionCool">
                <expand macro='matrix_h5_cooler_macro' />
                <param name='correctionName' type='text' label='Correction factors column name' />
                <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />

            </when>
            <when value="optionHomer">
                <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' />
            </when>
            <when value="optionHicpro">
                <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' />
                <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' />
            </when>
            <when value="option2Dtext">
                <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' />

                <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
                    <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
                </param>
                <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
            </when>
        </conditional>
    </xml>

    <xml name='convertFormat_multiple_macro'>

            <param name="inputFormat_selector" type="select" label="Choose input file type">
                <option value="optionCool" selected="True">cool</option>
                <option value="optionH5">h5</option>
                <option value="optionHomer">Homer</option>
                <option value="optionHicpro">HiCPro</option>
                <option value="option2Dtext">2D-text</option>


            </param>
            <when value="optionCool">
                <expand macro='matrix_h5_cooler_multiple_macro' />
                <param name='correctionName' type='text' label='Correction factors column name' />
                <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />

                <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' />
            </when>
            <when value="optionHicpro">
                <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' />
                <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' />
            </when>
            <when value="option2Dtext">
                <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' />

                <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
                    <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
                </param>
                <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
            </when>
        </conditional>
    </xml>
    <xml name='convertFormat_single_output_macro'>
        <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->

            <param name="outputFormat_selector" type="select" label="Choose output file type">
                <option value="cool" selected="True">cool</option>
                <option value="h5">h5</option>
                <option value="homer">Homer</option>
                <option value="ginteractions">ginteractions</option>
                <option value="hicpro">hicpro</option>

            </param>
            <when value="cool">
                <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
                <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
            </when>
            <when value='h5' />
            <when value='homer' />
            <when value='ginteractions' />
            <when value='hicpro' />
        </conditional>
    </xml>
    <token name="@REFERENCES@">

.. class:: infomark