Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions
changeset 4:38fa8a72ece6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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--- a/chicSignificantInteractions.xml Tue Mar 24 13:42:40 2020 -0400 +++ b/chicSignificantInteractions.xml Fri Aug 14 05:59:38 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.1"> <description>computes viewpoints with the given reference points and a background model</description> <macros> <token name="@BINARY@">chicSignificantInteractions</token> @@ -12,12 +12,17 @@ mkdir targetFolder && mkdir significantFilesFolder && - #for $file in $interactionFiles: - #set identifier = @ESCAPE_IDENTIFIER_FILE@ - - ln -s '$file' 'interactionFiles/$identifier' && - #end for - + #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 + #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) #end if @@ -53,9 +58,36 @@ --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> @@ -96,6 +128,8 @@ <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"> @@ -110,10 +144,19 @@ <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> </outputs> <tests> <test> - <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 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'/> @@ -149,7 +192,10 @@ <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/> </test> <test> - <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 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"/> @@ -174,6 +220,66 @@ <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> + <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" 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>
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