annotate chicExportData.xml @ 0:23b8d6b8960c draft

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

<tool id="hicexplorer_chicexportdata" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>exports data of hdf to txt based files</description>
    <macros>
        <token name="@BINARY@">chicExportData</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #import re
        mkdir exportFolder && 
        @BINARY@
            --file '$file'

            #if $fileType_conditional.fileType_selector == 'interaction':
                #if $fileType_conditional.txtBigwig_conditional.txtBigwig_selector == 'txt':
                    --outputFileType txt
                #else:
                    --outputFileType bigwig 
                    --outputValueBigwig $fileType_conditional.txtBigwig_conditional.column_selector
                    --chromosomeSizes '$fileType_conditional.txtBigwig_conditional.chromosomeSize'
                    --range $fileType_conditional.txtBigwig_conditional.rangeUpstream $fileType_conditional.txtBigwig_conditional.rangeDownstream
                    --backgroundModelFile '$fileType_conditional.txtBigwig_conditional.backgroundModelFile'
                #end if
            #else if $fileType_conditional.fileType_selector == 'target':
                $fileType_conditional.oneTargetFile
            #end if
            #if $fileType_conditional.fileType_selector != 'interaction':
                --outputFileType txt
            #end if

            --outputMode $outputMode_conditional.outputMode_selector
            #if $outputMode_conditional.outputMode_selector == 'geneName':
                --outputModeName $outputMode_conditional.outputModeName
            #end if
            --decimalPlaces $decimalPlaces
            
            --outFileName exportFolder/export.tar.gz
            --threads @THREADS@

    ]]>    </command>
    <inputs>

        <param name="file" type="data" format="h5" label="" />
        <conditional name="fileType_conditional">
       
            <param name="fileType_selector" type="select" label="Combination mode for the plots">
                <option value="interaction" selected="True">Interaction file (from chicViewpoint)</option>
                <option value="aggregate">Aggregated file (from chicAggregateStatistic)</option>
                <option value="significant" >Significant file (from chicSignificantInteractions)</option>
                <option value="target" >Target file (from chicSignificantInteractions)</option>
                <option value="differential" >Differential file (from chicDifferentialTest)</option>
            </param>
            <when value="interaction" >
                <conditional name="txtBigwig_conditional">
                    <param name="txtBigwig_selector" type="select" label="Output format">
                        <option value="txt" selected="True">Text</option>
                        <option value="bigwig">BigWig</option>
                    </param>
                    <when value="txt" >
                    </when>
                    <when value="bigwig" >
                        <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
                        <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
                        <param name="column_selector" type="select" label="Datatrack output type">
                            <option value="relative-interactions" selected="True">relative interactions</option>
                            <option value="p-value">p-value</option>
                            <option value="x-fold" >x-fold</option>
                            <option value="raw" >raw</option>
                        </param>
                        <param name="backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
                        <param name="chromosomeSize" type="data" format="tabular" label="Chromosome size" help="Chromosome size as tabular file. One chromosome per line" />
                    </when>
                </conditional>
            </when>
            <when value="aggregate" >
            </when>
            <when value="significant" >
            </when>
            <when value="target" >
                <param name="oneTargetFile" type="boolean" truevalue="--oneTargetFile" falsevalue="" checked="false" label="Create only one target file" />
            </when>
            <when value="differential" >
            </when>
        </conditional>

        <conditional name="outputMode_conditional">
            <param name="outputMode_selector" type="select" label="Output mode">
                <option value="all" selected="True">all</option>
                <option value="geneName" >gene name</option>
            </param>
            <when value="all" >
            </when>
            <when value="geneName" >
                <param name="outputModeName" type="text" value="" label="Gene name" help="Based on this gene name the output is extracted." />
            </when>
        </conditional>
        <param name="decimalPlaces" type="integer" value="12" label="Decimal places" help="Number of decimal places for float values." />

    </inputs>
    <outputs>
        <collection name="oneGeneCollectionBigwig" type="list" label="The exported bigwig files">
            <discover_datasets pattern="__name__" format="bigwig" directory="exportFolder" />
        </collection>
        <collection name="oneGeneCollectionText" type="list" label="The exported text files">
            <discover_datasets pattern="__name__" format="txt" directory="exportFolder" />
        </collection>
        <data name="allTar" from_work_dir="exportFolder/export.tar.gz" format="tar.gz" label="The exported data as tar.gz">
            <filter>outputMode_conditional['outputMode_selector'] == 'all'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="file" value="cHi-C/chicAggregateStatistic/aggregate.hdf5" />
            <conditional name="fileType_conditional">
                <param name="fileType_selector" value="aggregate" />
            </conditional>
            <conditional name="outputMode_conditional">
                <param name="outputMode_selector" value="all" />
            </conditional>
            <output name="allTar" file="cHi-C/chicExportData/aggregate.tar.gz" ftype="tar.gz" compare="sim_size" />
        </test>

        <test expect_num_outputs="2">
            <param name="file" value="cHi-C/chicViewpoint/two_matrices.hdf5" />
            <conditional name="fileType_conditional">
                <param name="fileType_selector" value="interaction" />
                
                <conditional name="txtBigwig_conditional">
                    <param name="txtBigwig_selector" value="bigwig" />
                    <param name="backgroundModelFile" value="cHi-C/background.txt" />
                    <param name="chromosomeSize" value="cHi-C/hg19.chrom.sizes" />
                </conditional>
            </conditional>
            <conditional name="outputMode_conditional">
                <param name="outputMode_selector" value="geneName" />
                <param name="outputModeName" value="Eya1" />
            </conditional>
            <output_collection name="oneGeneCollectionBigwig" type="list" count="4">
                <element name="background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" />
                <element name="background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" />
                <element name="FL-E13-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" />
                <element name="MB-E10-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" />
            </output_collection>
        </test>
        <test expect_num_outputs="2">
            <param name="file" value="cHi-C/chicViewpoint/two_matrices.hdf5" />
            <conditional name="fileType_conditional">
                <param name="fileType_selector" value="interaction" />
                <conditional name="txtBigwig_conditional">
                    <param name="txtBigwig_selector" value="txt" />
                </conditional>
            </conditional>
            <conditional name="outputMode_conditional">
                <param name="outputMode_selector" value="geneName" />
                <param name="outputModeName" value="Eya1" />
            </conditional>
            <output_collection name="oneGeneCollectionText" type="list" count="2">
                <element name="FL-E13-5_chr1_genes_Eya1_interactions.txt" file="cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1_interactions.txt" ftype="txt" compare="sim_size" />
                <element name="MB-E10-5_chr1_genes_Eya1_interactions.txt" file="cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1_interactions.txt" ftype="txt" compare="sim_size" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[

Exporting the binary data to text files
=======================================

chicExportData extracts the data stored in hdf5 files of the capture Hi-C modules to text files.

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>