Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions
diff chicSignificantInteractions.xml @ 6:6001400eed99 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 15:33:42 +0000 |
| parents | 38fa8a72ece6 |
| children | 640e0e45518a |
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--- a/chicSignificantInteractions.xml Fri Dec 11 21:43:10 2020 +0000 +++ b/chicSignificantInteractions.xml Tue Mar 16 15:33:42 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.1"> +<tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>computes viewpoints with the given reference points and a background model</description> <macros> <token name="@BINARY@">chicSignificantInteractions</token> @@ -17,8 +17,7 @@ tar -C interactionFiles -xvf viewpoints.tar && #else: #for $file in $tar_input_conditional.interactionFiles: - #set identifier = @ESCAPE_IDENTIFIER_FILE@ - + #set identifier = @ESCAPE_IDENTIFIER_FILE@ ln -s '$file' 'interactionFiles/$identifier' && #end for #end if @@ -30,9 +29,8 @@ #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': --interactionFile $interactonfileslist --computeSampleNumber $batchmode_conditional.computeSampleNumber - #else: - --interactionFile $batchmode_conditional.interactionFilesOrderFile + --interactionFile '$batchmode_conditional.interactionFilesOrderFile' --interactionFileFolder interactionFiles --batchMode --targetFileList targetListFile.txt @@ -71,7 +69,7 @@ && rm -rf significantFilesFolder #end if - ]]></command> + ]]> </command> <inputs> <conditional name="tar_input_conditional"> <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> @@ -79,29 +77,26 @@ <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"/> + <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"/> + <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."/> + <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."/> + <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='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> @@ -109,27 +104,23 @@ </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.'/> + 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. - 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 to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance. + 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 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." /> </inputs> <outputs> <collection name="significantFilesCollection" type="list" label="Significant files"> @@ -154,134 +145,182 @@ <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"/> + <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'/> + <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="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="backgroundModelFile" value="cHi-C/background.txt"/> - <param name="rangeUpstream" value="200000"/> - <param name="rangeDownstream" value="200000"/> + <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" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval" lines_diff="4"/> - <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval" lines_diff="4"/> - <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" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval" lines_diff="4"/> - <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" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval" lines_diff="4"/> + <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" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" ftype="interval" lines_diff="4"/> - <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" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" ftype="interval" lines_diff="4"/> + <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" compare="sim_size" delta='40000'/> - <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" 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='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"/> + <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"/> + <param name="batchmode_selector" value='optionSinglemode' /> + <param name="computeSampleNumber" value="1" /> </conditional> - <param name="pvalue" value='0.2'/> + <param name="pvalue" value='0.2' /> <conditional name="filter_conditional"> - <param name="filter_selector" value='optionXfold'/> - <param name="xfold" value='1.5'/> + <param name="filter_selector" value='optionXfold' /> + <param name="xfold" value='1.5' /> </conditional> - <param name="backgroundModelFile" value="cHi-C/background.txt"/> - <param name="rangeUpstream" value="200000"/> - <param name="rangeDownstream" value="200000"/> + <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" file="cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt" ftype="interval" lines_diff="4"/> + <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"/> + <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> - </test> + </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"/> + <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'/> + <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="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="backgroundModelFile" value="cHi-C/background.txt"/> - <param name="rangeUpstream" value="200000"/> - <param name="rangeDownstream" value="200000"/> + <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> - <param name='tar' value='True'/> + <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'/> + <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> - - <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[ @@ -298,6 +337,6 @@ For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html -]]></help> +]]> </help> <expand macro="citations" /> </tool>