comparison macros.xml @ 12:e89d515c3594 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"

11:0942d0a1b0bd

<macros>
    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
    <token name="@WRAPPER_VERSION@">2.1.4</token>
    <token name="@USE_RANGE@">
        #if $use_range.select_use_range == "yes_use_range":
            --range $range_min:$range_max
        #end if
    </token>

        <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.1133705</citation>

            <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="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="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"

    <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)]
            #end if
        #end for
        #set $mlabels = ' '.join($mlabels)
        #set $matrices = ' '.join($matrices)
    </token>


    <xml name="region">
        <param name="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" argument="--region"/>
    </xml>

            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="Matricies to compute on" multiple="true"/>
    </xml>
    <token name="@REFERENCES@">

.. class:: infomark

12:e89d515c3594

<macros>
    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
    <token name="@WRAPPER_VERSION@">3.3.1</token>
    <token name="@USE_RANGE@">
        #if $use_range.select_use_range == "yes_use_range":
            --range $range_min:$range_max
        #end if
    </token>

        <requirements>
            <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
            <yield />
        </requirements>
        <version_command>@BINARY@ --version</version_command>
    </xml>

    <token name="@CHROMOSOME_LIST@">
        #if $chromosome_list:
            #set $chromosomes = []
            #for $chrom in $chromosome_list:
                #silent $chromosomes.append("'%s'" % $chrom.chromosomes)
            #end for
            #set $chromosome_string = ' '.join($chromosomes)
            --chromosomes $chromosome_string
        #end if
    </token>

    <xml name="chromosome_list">
        <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included.">
            <param argument="--chromosomes" type="text" value="" >
                <validator type="empty_field" />
            </param>
        </repeat>
    </xml>

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

            <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="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="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="plasma_r">plasma reversed</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"

    <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
                #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
            #end if
        #end for
        #set $mlabels = ' '.join($mlabels)
        #set $matrices = ' '.join($matrices)
    </token>

    <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token>
    <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token>
    <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>

    <xml name="region">
        <param name="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" argument="--region"/>
    </xml>

            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="Matricies to compute on" multiple="true"/>
    </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'/>
                <param name='chromosome' type='text' label='Load only one chromosome'/>
                <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>

            </when>
            <when value="optionH5">
                <expand macro='matrix_h5_cooler_macro' />
            </when>
            <!-- <when value="optionHic">
                <param name='matrixHic' type='data' format='binary' label='.hic matrix'/>
                <param name='resolutions' type='text' label='List of resolutions'/>
            </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'>
        <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="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='chromosome' type='text' label='Load only one chromosome'/>
                <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>

            </when>
            <when value="optionH5">
                <expand macro='matrix_h5_cooler_multiple_macro' />
            </when>
           
            <when value="optionHomer">
                <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' multiple="true"/>
            </when>

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

        <conditional name="outputFormat_conditional">
            <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