comparison scHicAdjustMatrix.xml @ 1:799a9fe1265c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"

0:fad89d56674a

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

        --matrix '$matrix_mcooler'
        --action $action_selector
        #if $chromosomes:
            #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
            --chromosomes $chromosome
        #end if


        --outFileName adjusted_matrix.mcool

        --threads @THREADS@



    ]]></command>
    <inputs>
        
        <expand macro="matrix_mcooler_macro"/>
        <param name="action_selector" type="select" label="Action to take apply on matrices:">
                <option value="keep" selected="True">Keep the listed chromosomes</option>
                <option value="remove" >Remove the listed chromosomes</option>
        </param>
        <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="adjusted_matrix.mcool" format="mcool" label="${tool.name} on ${on_string}: merged matrix"/>
    </outputs>
    <tests>
        <test>
            <param name='matrix_mcooler' value='test_matrix.mcool' />
            <param name='clusterMethod_selector' value='keep' />
            <param name='chromosomes' value='chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX' />
            <output name="outFileName" ftype="mcool">
                <assert_contents>
                    <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name, 

    <help><![CDATA[

Adjust all matrices
===================

scHicAdjustMatrix is a tool to keep or remove a list of chromosomes of all Hi-C matrices stored in the mcool file.

For more information about scHiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://schicexplorer.readthedocs.io/
]]></help>

1:799a9fe1265c

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

        --matrix '$matrix_scooler'
        --action $action_selector
        #if $chromosomes:
            #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
            --chromosomes $chromosome
        #end if


        --outFileName adjusted_matrix.scool

        --threads @THREADS@



    ]]></command>
    <inputs>
        
        <expand macro="matrix_scooler_macro"/>
        <param name="action_selector" type="select" label="Action to take apply on matrices:">
                <option value="keep" selected="True">Keep the listed chromosomes</option>
                <option value="remove" >Remove the listed chromosomes</option>
        </param>
        <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="adjusted_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Adjusted matrix"/>
    </outputs>
    <tests>
        <test>
            <param name='matrix_scooler' value='test_matrix.scool' />
            <param name='clusterMethod_selector' value='keep' />
            <param name='chromosomes' value='chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX' />
            <output name="outFileName" ftype="scool">
                <assert_contents>
                    <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms, 
                    Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name, 

    <help><![CDATA[

Adjust all matrices
===================

scHicAdjustMatrix is a tool to keep or remove a list of chromosomes of all Hi-C matrices stored in the scool file.

For more information about scHiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://schicexplorer.readthedocs.io/
]]></help>