annotate hicPlotDistVsCounts.xml @ 5:819bd2c44d4a draft

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

<tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>distance vs HiC counts plot per chromosome</description>
    <macros>
        <token name="@BINARY@">hicPlotDistVsCounts</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
        #import re
        #set matrices_path=[]
        #set matrices_labels=[]
        #for $counter, $m, in enumerate($matrices):
            #set identifier = re.sub('[^\s\w\-]', '_', str($m.element_identifier))
            ln -f -s '${m}' '${identifier}_${counter}' &&
            #silent $matrices_path.append("'%s_%s'" % ($identifier, $counter))
            #silent $matrices_labels.append("'%s'" % ($identifier))
        #end for

        @BINARY@
            --matrices #echo " ".join($matrices_path)#
            --labels #echo " ".join($matrices_labels)#
            $skipDiagonal
            --plotFile plot.png
            #if $plotsize:
                --plotsize $plotsize
            #end if
            --maxdepth $maxdepth
            $perchr
            #set chroms = " ".join([ "'%s'" % $var.chromosomeExclude for $var in $chromosomeExclude ])
            #if $chromosomeExclude:
                --chromosomeExclude '$chroms'
            #end if
]]>
    </command>
    <inputs>
        <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="HiC normalized (corrected) matrices"/>

        <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" />
        <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome"
            help="If more than one HiC matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." />
        <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth"
            help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." />
        <param argument="--plotsize" type="text" optional="True" label="Plot size"
            help="Width and height of the plot (in inches). Default is 6*number of cols, 4 * number of rows. The maximum number of rows is 4. Example --plotsize 6 5." />
        <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude"
            help="This is useful for example to exclude the Y chromosome.">
            <param argument="--chromosomeExclude" type="text" value="" >
                <validator type="empty_field" />
            </param>
        </repeat>

    </inputs>
    <outputs>
        <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
            <param name="skipDiagonal" value="False"/>
            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5,small_test_matrix_50kb_res.h5"/>
            <param name="skipDiagonal" value="False"/>
            <param name="perchr" value="True" />
            <repeat name="chromosomeExclude">
                <param name="chromosomeExclude" value="chrUextra"/>
            </repeat>
            <repeat name="chromosomeExclude">
                <param name="chromosomeExclude" value="chrM"/>
            </repeat>
            <repeat name="chromosomeExclude">
                <param name="chromosomeExclude" value="chr3LHet"/>
            </repeat>
            <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/>
        </test>
    </tests>
    <help><![CDATA[
Relation of genomic distance and number of contacts
========================================================

| This program makes a distance vs. Hi-C counts plots. It can use several matrix files to compare
| them. If the ``--perchr`` option is given, each chromosome is plotted independently. In the case
| of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple
| matrices denser matrices are scaled down to match the sum of the smaller matrix.
|
| For more information about HiCExplorer please consider our documentation on readthedocs.io_


Input
-----

Parameters
__________
- contact matrix
- skip diagonal
- per chromosome
- max depth
- plot size
- chromosome(s) to exclude

Output
-------
Output if all data in the contact matrix is considered:

.. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result1.png
   :width: 70%

Output if the distance vs. Hi-C contact counts is computed and plotted per chromosome:

.. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result2.png
   :width: 80% 

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
]]></help>
    <expand macro="citations" />
</tool>