comparison hicAggregateContacts.xml @ 5:ce16a538ab46 draft

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

4:0c812ed34277

        <token name="@BINARY@">hicAggregateContacts</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
@BINARY@
    --matrix '$matrix_h5_cooler'
    --BED $BED
    #if $BED2:
        --BED2 $BED2
    #end if

    --range $range_min:$range_max

    --numberOfBins $numberOfBins

    --transform $transform
    --avgType $avgType

    #if $outputs and 'PrefixMatrix' in $outputs:

            help= "Maximum value of the plotted score." />

        <param name="image_file_format" type="select" label="Image output format">
            <option value="png" selected="True">png</option>
            <option value="svg">svg</option>
        </param>

        <param name="outputs" type="select" optional="true" multiple="true" label="Optional output files">
            <option value="PrefixMatrix">Save values underlying the final matrix</option>
            <option value="ClusterContactPositions">Save the position of the contacts</option>

    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}: Plot">
            <change_format>
                <when input="image_file_format" value="svg" format="svg" />
            </change_format>
        </data>
        <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values">
            <discover_datasets pattern="matrix_values_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
        </collection>

            <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5" ftype="h5"/>
            <param name="BED" value="test_regions.bed" ftype="bed"/>
            <param name="numberOfBins" value="30" />
            <param name="range_max" value="900000" />
            <param name="range_min" value="50000" />
            <param name="image_file_format" value="png" />
            <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
Aggregation of Hi-C contacts
============================

5:ce16a538ab46

        <token name="@BINARY@">hicAggregateContacts</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
    @BINARY@
    --matrix 'matrix.$matrix_h5_cooler.ext'
    --BED $BED
    #if $BED2:
        --BED2 $BED2
    #end if

    --range '$range_min:$range_max'

    --numberOfBins '$numberOfBins'

    --transform $transform
    --avgType $avgType

    #if $outputs and 'PrefixMatrix' in $outputs:

            help= "Maximum value of the plotted score." />

        <param name="image_file_format" type="select" label="Image output format">
            <option value="png" selected="True">png</option>
            <option value="svg">svg</option>
            <option value="pdf">pdf</option>

        </param>

        <param name="outputs" type="select" optional="true" multiple="true" label="Optional output files">
            <option value="PrefixMatrix">Save values underlying the final matrix</option>
            <option value="ClusterContactPositions">Save the position of the contacts</option>

    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}: Plot">
            <change_format>
                <when input="image_file_format" value="svg" format="svg" />
                <when input="image_file_format" value="pdf" format="pdf" />

            </change_format>
        </data>
        <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values">
            <discover_datasets pattern="matrix_values_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
        </collection>

            <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool"/>
            <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed"/>
            <param name="numberOfBins" value="30" />
            <param name="range_max" value="900000" />
            <param name="range_min" value="50000" />
            <param name="image_file_format" value="png" />
            <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" delta='35000'/>
        </test>
    </tests>
    <help><![CDATA[
Aggregation of Hi-C contacts
============================