Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions
diff chicSignificantInteractions.xml @ 8:640e0e45518a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
| author | iuc |
|---|---|
| date | Wed, 18 Oct 2023 10:52:55 +0000 |
| parents | 6001400eed99 |
| children |
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--- a/chicSignificantInteractions.xml Tue Jan 10 18:50:07 2023 +0000 +++ b/chicSignificantInteractions.xml Wed Oct 18 10:52:55 2023 +0000 @@ -7,37 +7,11 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ #import re - - mkdir interactionFiles && - mkdir targetFolder && - mkdir significantFilesFolder && - - #if $tar_input_conditional.tar_input_selector == 'tar_input': - ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && - tar -C interactionFiles -xvf viewpoints.tar && - #else: - #for $file in $tar_input_conditional.interactionFiles: - #set identifier = @ESCAPE_IDENTIFIER_FILE@ - ln -s '$file' 'interactionFiles/$identifier' && - #end for - #end if + + @BINARY@ - #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': - #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) - #end if - @BINARY@ - #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': - --interactionFile $interactonfileslist - --computeSampleNumber $batchmode_conditional.computeSampleNumber - #else: - --interactionFile '$batchmode_conditional.interactionFilesOrderFile' - --interactionFileFolder interactionFiles - --batchMode - --targetFileList targetListFile.txt - --writeFileNamesToFile significantFiles.txt - --computeSampleNumber $batchmode_conditional.computeSampleNumber - #end if - + --interactionFile '$interactionFile' + --pValue $pvalue #if $filter_conditional.filter_selector == 'optionXfold': @@ -47,280 +21,84 @@ #end if --backgroundModelFile '$backgroundModelFile' - --resolution $resolution --peakInteractionsThreshold $peakInteractionsThreshold --range $rangeUpstream $rangeDownstream - --targetFolder targetFolder - --outputFolder significantFilesFolder + --combinationMode $mode_selector + --outFileNameSignificant significant.hdf5 + --outFileNameTarget target.hdf5 $truncateZeroPvalues --fixateRange $fixateRange - -suffix significant_interactions.txt --threads @THREADS@ - #if $tar: - && cd targetFolder - && tar -cvf ../targetFolder.tar * - && cd .. - && rm -rf targetFolder - - && cd significantFilesFolder - && tar -cvf ../significantFilesFolder.tar * - && cd .. - && rm -rf significantFilesFolder - - #end if ]]> </command> <inputs> - <conditional name="tar_input_conditional"> - <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> - <option value="tar_input">Tar file</option> - <option value="interval_input" selected="True">Interval files</option> - </param> - <when value="tar_input"> - <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" /> - </when> - <when value="interval_input"> - <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true" /> - </when> - </conditional> - <conditional name="batchmode_conditional"> - <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> - <option value="optionBatchmode">Batch processing</option> - <option value="optionSinglemode" selected="True">Single file processing</option> - </param> - <when value="optionBatchmode"> - <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" /> - <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files." /> - </when> - <when value="optionSinglemode"> - <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files." /> - </when> - </conditional> - <param name='pvalue' type="float" value='0.05' label="P-value of interaction to be accepted as significant" /> + <param name="interactionFile" type="data" format="h5" label="The interaction data file created by chicViewpoint" /> + + <param name="pvalue" type="float" value="0.05" label="P-value of interaction to be accepted as significant" /> <conditional name="filter_conditional"> <param name="filter_selector" type="select" label="List of chromosomes or a BED file containg regions"> <option value="optionXfold">x-fold over mean background</option> <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option> </param> <when value="optionXfold"> - <param name='xfold' type="float" value='2.0' label="X-fold over mean background to be accepted." help='Filter x-fold over background. Used to merge neighboring bins with a broader peak but - less significant interactions to one peak with high significance. Used only for pValue option.' /> + <param name="xfold" type="float" value="2.0" label="X-fold over mean background to be accepted." help="Filter x-fold over background. + Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance. Used only for pValue option." /> </when> <when value="optionLoosePvalue"> - <param name='loosePvalue' type="float" value='0.3' label="Loose p-value" help='loose p-value threshold value to filter target regions in a first round. + <param name="loosePvalue" type="float" value="0.3" label="Loose p-value" help="loose p-value threshold value to filter target regions in a first round. Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance. - Used only for pValue option.' /> + Used only for pValue option." /> </when> </conditional> - <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" /> - <param argument="--peakInteractionsThreshold" type="integer" value="5" label="Minimum interactions" help='The minimum number of interactions a detected peaks needs to have to be considered.' /> - <param argument="--resolution" type="integer" value="1000" label="Bin resolution of the used data" help='Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution. - This value is used to merge neighboring bins.' /> - <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 argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.' /> - <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one." help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision." /> - <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file" help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large." /> + + <param argument="--backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" /> + <param argument="--peakInteractionsThreshold" type="integer" value="5" label="Minimum interactions" help="The minimum number of interactions a detected peaks needs to have to be considered." /> + + <param name="mode_selector" type="select" label="Process matrices independently or combine always two (for differential analysis preparation)"> + <option value="dual">Dual</option> + <option value="single" selected="True">Single</option> + </param> + <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 argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help="Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin." /> + <param name="truncateZeroPvalues" type="boolean" truevalue="--truncateZeroPvalues" falsevalue="" checked="false" label="Truncate zeros by setting them to one." help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision." /> </inputs> + <outputs> - <collection name="significantFilesCollection" type="list" label="Significant files"> - <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" /> - </collection> - <collection name="targetFilesCollection" type="list" label="Target files"> - <discover_datasets pattern="__name__" format="interval" directory="targetFolder" /> - </collection> - <data name="significantFileNames" from_work_dir="significantFiles.txt" format="txt" label="${tool.name} significant file names"> - <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> - </data> - <data name="targetFileNames" from_work_dir="targetListFile.txt" format="txt" label="${tool.name} target file names"> - <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> - </data> - <data name="targetFolderTar" from_work_dir="targetFolder.tar" format="tar" label="Target files tar"> - <filter>tar</filter> - </data> - <data name="significantFilesFolderTar" from_work_dir="significantFilesFolder.tar" format="tar" label="Significant files tar"> - <filter>tar</filter> - </data> + <data name="significantFile" from_work_dir="significant.hdf5" format="h5" label="${tool.name} significant file" /> + <data name="targetFile" from_work_dir="target.hdf5" format="h5" label="${tool.name} target file" /> </outputs> <tests> <test> - <conditional name="tar_input_conditional"> - <param name="tar_input_selector" value='interval_input' /> - <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" /> - </conditional> - <conditional name="batchmode_conditional"> - <param name="batchmode_selector" value='optionBatchmode' /> - <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> - <param name="computeSampleNumber" value='2' /> - </conditional> - <param name="pvalue" value='0.2' /> + <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" /> + <param name="pvalue" value="0.2" /> <conditional name="filter_conditional"> - <param name="filter_selector" value='optionLoosePvalue' /> - <param name="loosePvalue" value='0.5' /> + <param name="filter_selector" value="optionLoosePvalue" /> + <param name="loosePvalue" value="0.5" /> </conditional> - + <param name="mode_selector" value="dual" /> <param name="backgroundModelFile" value="cHi-C/background.txt" /> <param name="rangeUpstream" value="200000" /> <param name="rangeDownstream" value="200000" /> - <output_collection name="significantFilesCollection" type="list" count="6"> - <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval"> - <assert_contents> - <has_text text="4480000" /> - <has_text text="chr1" /> - <has_text text="Sox17" /> - <has_text text="810.0" /> - <has_text text="interactions" /> - </assert_contents> - </element> - <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval"> - <assert_contents> - <has_text text="14274000" /> - <has_text text="chr1" /> - <has_text text="Eya1" /> - <has_text text="interactions" /> - </assert_contents> - </element> - <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval" lines_diff="4" /> - <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval"> - <assert_contents> - <has_text text="4480000" /> - <has_text text="chr1" /> - <has_text text="Sox17" /> - <has_text text="interactions" /> - <has_text text="93000" /> - <has_text text="978.0" /> - </assert_contents> - </element> - <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval" lines_diff="4" /> - <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval"> - <assert_contents> - <has_text text="19077000" /> - <has_text text="chr1" /> - <has_text text="Tfap2d" /> - <has_text text="interactions" /> - <has_text text="-15000" /> - </assert_contents> - </element> - </output_collection> - <output_collection name="targetFilesCollection" type="list" count="3"> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" ftype="interval"> - <assert_contents> - <has_text text="4555000" /> - <has_text text="chr1" /> - <has_text text="p-value" /> - <has_text text="interactions" /> - </assert_contents> - </element> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4" /> - <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" ftype="interval"> - <assert_contents> - <has_text text="19143000" /> - <has_text text="chr1" /> - <has_text text="p-value" /> - <has_text text="19150000" /> - </assert_contents> - </element> - </output_collection> - <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" /> - <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" /> - </test> - <test> - <conditional name="tar_input_conditional"> - <param name="tar_input_selector" value='interval_input' /> - <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" /> - </conditional> - <conditional name="batchmode_conditional"> - <param name="batchmode_selector" value='optionSinglemode' /> - <param name="computeSampleNumber" value="1" /> - </conditional> - <param name="pvalue" value='0.2' /> - - <conditional name="filter_conditional"> - <param name="filter_selector" value='optionXfold' /> - <param name="xfold" value='1.5' /> - </conditional> + <output name="significantFile" ftype="h5"> + <assert_contents> + <has_h5_attribute key="combinationMode" value="dual" /> + <has_h5_attribute key="mode_preselection" value="loosePValue" /> + <has_h5_attribute key="type" value="significant" /> + </assert_contents> + </output> - <param name="backgroundModelFile" value="cHi-C/background.txt" /> - <param name="rangeUpstream" value="200000" /> - <param name="rangeDownstream" value="200000" /> - - <output_collection name="significantFilesCollection" type="list" count="2"> - <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt" ftype="interval" lines_diff="4" /> - <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval"> - <assert_contents> - <has_text text="14295000" /> - <has_text text="chr1" /> - <has_text text="Eya1" /> - <has_text text="interactions" /> - </assert_contents> - </element> - </output_collection> - <output_collection name="targetFilesCollection" type="list" count="2"> - <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4" /> - <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4" /> - </output_collection> + <output name="targetFile" ftype="h5"> + <assert_contents> + <has_h5_attribute key="combinationMode" value="dual" /> + <has_h5_attribute key="mode_preselection" value="loosePValue" /> + <has_h5_attribute key="type" value="target" /> + </assert_contents> + </output> </test> - - <test> - <conditional name="tar_input_conditional"> - <param name="tar_input_selector" value='interval_input' /> - <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" /> - </conditional> - <conditional name="batchmode_conditional"> - <param name="batchmode_selector" value='optionBatchmode' /> - <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> - <param name="computeSampleNumber" value='2' /> - </conditional> - <param name="pvalue" value='0.2' /> - - <conditional name="filter_conditional"> - <param name="filter_selector" value='optionLoosePvalue' /> - <param name="loosePvalue" value='0.5' /> - </conditional> - - <param name="backgroundModelFile" value="cHi-C/background.txt" /> - <param name="rangeUpstream" value="200000" /> - <param name="rangeDownstream" value="200000" /> - - <param name='tar' value='True' /> - - <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> - <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> - <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" /> - <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" /> - </test> - - <test> - <conditional name="tar_input_conditional"> - <param name="tar_input_selector" value='tar_input' /> - <param name="interactionFiles" value="cHi-C/chicViewpoint/viewpoints.tar" /> - </conditional> - <conditional name="batchmode_conditional"> - <param name="batchmode_selector" value='optionBatchmode' /> - <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> - <param name="computeSampleNumber" value='2' /> - </conditional> - <param name="pvalue" value='0.2' /> - - <conditional name="filter_conditional"> - <param name="filter_selector" value='optionLoosePvalue' /> - <param name="loosePvalue" value='0.5' /> - </conditional> - - <param name="backgroundModelFile" value="cHi-C/background.txt" /> - <param name="rangeUpstream" value="200000" /> - <param name="rangeDownstream" value="200000" /> - - <param name='tar' value='True' /> - - <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> - <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> - - <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000' /> - <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000' /> - </test> + </tests> <help><![CDATA[