Mercurial > repos > iuc > hicexplorer_chicexportdata
diff chicExportData.xml @ 0:ee7fd64f00eb draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
| author | iuc |
|---|---|
| date | Wed, 18 Oct 2023 10:31:51 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chicExportData.xml Wed Oct 18 10:31:51 2023 +0000 @@ -0,0 +1,175 @@ +<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>