comparison hicAdjustMatrix.xml @ 8:2dccb6bb0add draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

7:aeacaf08bd52

        #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionRegionFile":
            --regions '$chromosomeOrRegionFile_conditional.regions'
        #end if

        && mv '$matrix_file_out' matrix
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />
        <param name="action_selector" type="select" label="Apply action">
            <option value="keep" selected="True">keep</option>
            <option value="remove">remove</option>
            <option value="mask">mask</option>
        </param>

            </when>
            <when value="optionRegionFile">
                <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered" help="Should contain the regions which should be kept, removed or masked." />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="matrix" format="h5">
            <change_format>
                <when input="matrix_h5_cooler.ext" value="cool" format="cool" />

    <tests>
        <test expect_num_outputs="1">
            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
            <param name="action_selector" value="keep" />
            <conditional name="chromosomeOrRegionFile_conditional">
                <param name="chromosomeOrRegionFile_selector" value='optionChromosomes' />
                <repeat name="chromosomeOrder">
                    <param name="chromosome" value='chrX' />
                    <param name="chromosome" value='chr3R' />
                </repeat>
            </conditional>
            <output name="outFileName" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys='intervals,matrix' />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
            <param name="action_selector" value="mask" />
            <conditional name="chromosomeOrRegionFile_conditional">
                <param name="chromosomeOrRegionFile_selector" value='optionRegionFile' />
                <param name="regions" value='regions.bed' />
            </conditional>
            <output name="outFileName" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys='intervals,matrix,nan_bins' />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

8:2dccb6bb0add

        #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionRegionFile":
            --regions '$chromosomeOrRegionFile_conditional.regions'
        #end if

        #if not $interIntra_selector == 'keep':
            --interIntraHandling $interIntra_selector
        #end if
        && mv '$matrix_file_out' matrix

]]>
    </command>
    <inputs>
        <expand macro="matrix_h5_cooler_macro" />
        <param name="action_selector" type="select" label="Apply action">
            <option value="keep" selected="True">keep</option>
            <option value="remove">remove</option>
            <option value="mask">mask</option>
        </param>

            </when>
            <when value="optionRegionFile">
                <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered" help="Should contain the regions which should be kept, removed or masked." />
            </when>
        </conditional>
        <param name="interIntra_selector" type="select" label="Remove inter- or intra chromosomal regions">
            <option value="keep" selected="True">Do not apply</option>
            <option value="inter">Remove inter-chromosomal contacts</option>
            <option value="intra">Remove intra-chromosomal contacts</option>
        </param>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="matrix" format="h5">
            <change_format>
                <when input="matrix_h5_cooler.ext" value="cool" format="cool" />

    <tests>
        <test expect_num_outputs="1">
            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
            <param name="action_selector" value="keep" />
            <conditional name="chromosomeOrRegionFile_conditional">
                <param name="chromosomeOrRegionFile_selector" value="optionChromosomes" />
                <repeat name="chromosomeOrder">
                    <param name="chromosome" value="chrX" />
                    <param name="chromosome" value="chr3R" />
                </repeat>
            </conditional>
            <output name="outFileName" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys="intervals,matrix" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
            <param name="action_selector" value="mask" />
            <conditional name="chromosomeOrRegionFile_conditional">
                <param name="chromosomeOrRegionFile_selector" value="optionRegionFile" />
                <param name="regions" value="regions.bed" />
            </conditional>
            <output name="outFileName" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys="intervals,matrix,nan_bins" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[