Mercurial > repos > bgruening > hicexplorer_chicexportdata
view chicExportData.xml @ 2:cab616fe7e64 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
author | iuc |
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date | Mon, 04 Nov 2024 23:50:05 +0000 |
parents | 163fd744e235 |
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<tool id="hicexplorer_chicexportdata" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <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="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" /> <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" /> </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>