comparison hicBuildMatrix.xml @ 5:3bc1425f9000 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5

4:652fdcbff650

            #end for

            #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile":
                --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile'
                --minDistance $restrictionCutFileBinSize_conditional.minDistance
                --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize          
            #end if

            #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
                --binSize $restrictionCutFileBinSize_conditional.binSize
            #end if

            #if $region:
                --region '$region'
            #end if

            --outFileName ./matrix.h5
            --outBam ./unsorted.bam

            $keepSelfCircles

            #if $minMappingQuality and $minMappingQuality is not None:

                    the dangling end is the same restriction sequence. This is used
                    to discard reads that end/start with such sequence 
                    and that are considered un-ligated fragments or 
                    'dangling-ends'. If not given, such statistics will 
                    not be available."/>
    </inputs>
    <outputs>
        <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
        <data name="outFileName" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/>
        <data name="qc" format="html" label="${tool.name} QC"/>
    </outputs>
    <tests>
        <test>
            <repeat name="samFiles">
                <param name="samFile" value="small_test_R1_unsorted.bam" ftype="sam" />
            </repeat>
            <repeat name="samFiles">
                <param name="samFile" value="small_test_R2_unsorted.bam" ftype="sam"/>
            </repeat>
            <conditional name="restrictionCutFileBinSize_conditional">
                <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
                <param name="binSize" value="5000"/>
            </conditional>
            <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
            <output name="outFileName" file="small_test_matrix.h5" ftype="h5" compare="sim_size" delta="30000"/>
        </test>
    </tests>
    <help><![CDATA[

Creation of the contact matrix
===============================

``hicBuildMatrix`` creates a contact matrix based on Hi-C read pairs. It requires two sam or bam files 
corresponding to the first and second mates of the paired-end H-C reads. The sam and bam files should
 not be sorted by position. There are two main options to create the Hi-C contact matrix, either by 
fixed bin size (eg. 10.000 bp) or by bins of variable restriction fragment size length. 
``hicBuildMatrix`` generates a quality control output that can be used to analyze the quality of the Hi-C reads.

Input
-----

- right pairs 

.. image:: $PATH_TO_IMAGES/hicQC.png
   :width: 70 %

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

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html

5:3bc1425f9000

            #end for

            #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile":
                --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile'
                --minDistance $restrictionCutFileBinSize_conditional.minDistance
                --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize
            #end if

            #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
                --binSize $restrictionCutFileBinSize_conditional.binSize
            #end if

            #if $region:
                --region '$region'
            #end if

            #if $outputFormat == 'h5'
                --outFileName matrix.h5
            #elif $outputFormat == 'cool'
                --outFileName matrix.cool
            #end if
            --outBam ./unsorted.bam

            $keepSelfCircles

            #if $minMappingQuality and $minMappingQuality is not None:

                    the dangling end is the same restriction sequence. This is used
                    to discard reads that end/start with such sequence 
                    and that are considered un-ligated fragments or 
                    'dangling-ends'. If not given, such statistics will 
                    not be available."/>
        <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="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
        <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}">
            <filter>outputFormat == 'h5'</filter>
        </data>
        <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool" label="${tool.name} MATRIX on ${on_string}">
            <filter>outputFormat == 'cool'</filter>
        </data>
        <data name="qc" format="html" label="${tool.name} QC"/>
    </outputs>
    <tests>
        <test>
            <repeat name="samFiles">
                <param name="samFile" value="small_test_R1_unsorted.sam"/>
            </repeat>
            <repeat name="samFiles">
                <param name="samFile" value="small_test_R2_unsorted.sam"/>
            </repeat>
            <conditional name="restrictionCutFileBinSize_conditional">
                <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
                <param name="binSize" value="5000"/>
            </conditional>
            <param name='outputFormat' value='h5'/>

            <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
            <output name="outFileName_h5" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

Creation of the contact matrix
===============================

``hicBuildMatrix`` creates a contact matrix based on Hi-C read pairs. It requires two sam or bam files 
corresponding to the first and second mates of the paired-end H-C reads. The sam and bam files should 
not be sorted by position. There are two main options to create the Hi-C contact matrix, either by 
fixed bin size (eg. 10.000 bp) or by bins of variable restriction fragment size length. 
``hicBuildMatrix`` generates a quality control output that can be used to analyze the quality of the Hi-C reads.

Input
-----

- right pairs 

.. image:: $PATH_TO_IMAGES/hicQC.png
   :width: 70 %


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

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html