comparison hicSumMatrices.xml @ 14:34ea556ba897 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"

13:2f18082f828b

    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
            ln -s '$m' ${counter}_matrix &&
        #end for
        #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])

        hicSumMatrices
            --matrices "$m"
            --outFileName matrix.$outputFormat

        && mv matrix.$outputFormat matrix
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_multiple_macro'/>

        <param name='outputFormat' type='select' label="Output file format">
            <option value='h5'>HiCExplorer format</option>
            <option value="cool">cool</option>
        </param>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="matrix" format="h5">
             <change_format>
                <when input="outputFormat" value="cool" format="cool" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler_multiple" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/>
            <!-- <param name="matrices" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/> -->
            <param name='outputFormat' value='h5'/>
            <output name="outFileName" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/>
        </test>
    </tests>
    <help><![CDATA[
Summation of matrices
=====================

14:34ea556ba897

    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
            ln -s '$m' '${counter}_matrix.$m.ext' &&
        #end for
        #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
        #set $extension = $matrix_h5_cooler_multiple[0].ext
        @BINARY@
            --matrices $m
            --outFileName 'matrix.$extension'

        && mv 'matrix.$extension' matrix
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_multiple_macro'/>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="matrix" format_source='matrix_h5_cooler_multiple'/>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/>

            <output name="outFileName" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys='intervals,matrix'/>
                </assert_contents>
            </output>
        </test>
         <test>
            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool"/>

            <output name="outFileName" ftype="cool">
                <assert_contents>
                    <has_h5_keys keys='bins,chroms,indexes,pixels'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Summation of matrices
=====================