annotate hicValidateLocations.xml @ 8:1d201e8378b3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

<tool id="hicexplorer_hicvalidatelocations" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>validate detected loops with protein peaks.</description>
    <macros>
        <token name="@BINARY@">hicValidateLocations</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @BINARY@
            --data '$data'
            --validationData '$validationData'
            --validationType '$validationData.ext'
            --method $method_selector
            --resolution '$resolution'
            #if not $prefixLoop_selector == 'keep':
                 --chrPrefixLoops $prefixLoop_selector
            #end if
            #if not $prefixProtein_selector == 'keep':
                 --chrPrefixProtein $prefixProtein_selector
            #end if
           
            --outFileName outfile
    ]]>    </command>
    <inputs>
        <param argument="--data" type="data" format="bed" label="Loop file" help="The loop file from hicDetectLoops. To use files from other sources, please follow 'chr start end chr start end' format." />
        <param argument="--validationData" type="data" format="bed,cool" label="Validation data" help="The protein peak file or a cool file containing e.g. HiChIP information" />
        <param name="method_selector" type="select" label="Validate loop or TAD data">
            <option value="loops" selected="True">Loops</option>
            <option value="tad">TADs</option>
        </param>
        <param argument="--resolution" type="integer" value="" label="Used resolution" help="The to be binned resolution." />
        <param name="prefixLoop_selector" type="select" label="Add, remove, or keep the chr-prefix of the loop/TAD data">
            <option value="keep" selected="True">Keep</option>
            <option value="add">Add</option>
            <option value="remove">Remove</option>

        </param>

        <param name="prefixProtein_selector" type="select" label="Add, remove, or keep the chr-prefix of the validation data">
            <option value="keep" selected="True">Keep</option>
            <option value="add">Add</option>
            <option value="remove">Remove</option>
        </param>
    </inputs>
    <outputs>
        <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic" />
        <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations" />
    </outputs>
    <tests>
        <test>
            <param name="data" ftype="bed" value="hicValidateLocations/loops_1.bedgraph" />
            <param name="validationData" ftype="bed" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />
            <param name="resolution" value="10000" />
            <param name="prefixLoop_selector" value="add" />
            <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" lines_diff="2" />
            <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" lines_diff="4" />
        </test>
    </tests>
    <help><![CDATA[

Validate locations
==================

This script overlaps the loop locations with protein locations to determine the accuracy of the loop detection.
Loops need to have format as follows:

`chr start end chr start end`

The protein peaks need to be in narrowPeaks or broadPeak format.

A protein match is successfull if at the bin of the x and y location a protein peak is overlapped.
A bin is assumed to have a protein if one or more protein peaks falling within the bin region.
The value of the protein is not considered, only match or non-match.

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>