annotate hicMergeDomains.xml @ 0:6b9b4fd51308 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"

<tool id="hicexplorer_hicmergedomains" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Merges TAD domains</description>
    <macros>
        <token name="@BINARY@">hicMergeDomains</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        
            #for $counter, $tadfile in enumerate($domainFiles):
                ln -s '$tadfile' '${counter}_tad_file.bed' &&
            #end for
            #set $m = ' '.join([ '\'%s_tad_file.bed\'' % $counter for $counter, $inputfile in enumerate($domainFiles) ])
            
            @BINARY@        
            
            --domainFiles $m
            
            #if $proteinFile:
                --proteinFile '$proteinFile'
            #end if

            #if $minimumNumberOfPeaks:
                --minimumNumberOfPeaks $minimumNumberOfPeaks
            #end if

            #if $valueX:
                --value $valueX
            #end if

            #if $percent:
                --percent $percent
            #end if

            --outputMergedList mergedDomains.bed
            --outputRelationList relationList.txt
            --outputTreePlotFormat pdf
            --outputTreePlotPrefix relationship_tree

            && mkdir relationship_plots
            && cp relationship_tree_*.pdf relationship_plots
]]>
    </command>
    <inputs>
        <param name="domainFiles" type='data' format="bed" multiple="true" label="Domain files from hicFindTADs of different resolutions to include" />
        <param argument="--proteinFile" type='data' format="bed" label="Protein peak file in bed format" help= "In order to be able to better assess the relationship between TADs, the associated protein file (e.g. CTCF for mammals) can be included. The protein file is required in broadpeak forma" />
        <param argument="--minimumNumberOfPeaks" type="integer" label="Minimum number of peaks" help="Optional parameter to adjust the number of protein peaks when adapting the resolution to the domain files. At least minimumNumberOfPeaks of unique peaks must be in a bin to considered. Otherwise the bin is treated like it has no peaks" value='1' />
        <param argument="--valueX" type="integer" label="TAD seperation value" help="Determine a value by how much the boundaries of two TADs must at least differ to consider them as two separate TADs" value='5000' />
        <param argument="--percent" type="float" label="Percentage overlap" help="For the relationship determination, a percentage is required from which area coverage the TADs are related to each other. For example, a relationship should be entered from 5 percent area coverage" value="0.5" />
    </inputs>
    <outputs>
        <data name='outputMergedList' from_work_dir='mergedDomains.bed' format='bed' label='Merged domains' />
        <data name='outputRelationList' from_work_dir='relationList.txt' format='txt' label='Relationship list' />
        <collection name="plotCollection" type="list" label="Relationship tree plots">
            <discover_datasets pattern="__name__" format='pdf' directory="relationship_plots" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="domainFiles" ftype='bed' value="hicMergeDomains/10kbtad_domains.bed,hicMergeDomains/50kbtad_domains.bed,hicMergeDomains/100kbtad_domains.bed" />

            <param name="minimumNumberOfPeaks" value="2" />
            <param name="proteinFile" value="hicMergeDomains/ctcf_sorted.bed" />
            <param name="valueX" value="5000" />
            <param name="percent" value="0.7" />
            <output name="outputMergedList" file="hicMergeDomains/merged_list.bed" ftype="bed" />
            <output name="outputRelationList" file="hicMergeDomains/relationship.txt" ftype="txt" />

            <output_collection name="plotCollection" type="list" count="1">
                <element name="relationship_tree_1.pdf" file="hicMergeDomains/ctcf_plot/two_files_plot_1.pdf" ftype="pdf" compare="sim_size" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[

Merge of TAD domains
====================

Merges and computes the hierachy of TADs from different resolutions.

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

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

]]>    </help>
    <expand macro="citations" />
</tool>