Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic
diff chicAggregateStatistic.xml @ 6:b53973719d7b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 15:19:00 +0000 |
| parents | d6f5e51e97ec |
| children | 01c37e54e86e |
line wrap: on
line diff
--- a/chicAggregateStatistic.xml Fri Dec 11 21:29:31 2020 +0000 +++ b/chicAggregateStatistic.xml Tue Mar 16 15:19:00 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@WRAPPER_VERSION@.1"> +<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>computes with a target file the to be tested regions for chicDifferentialTest</description> <macros> <token name="@BINARY@">chicAggregateStatistic</token> @@ -11,7 +11,6 @@ mkdir targetFolder && mkdir aggregatedFilesFolder && - #if $tar_input_conditional.tar_input_selector == 'tar_input': ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && tar -C interactionFiles -xvf viewpoints.tar && @@ -30,14 +29,11 @@ #set identifier = @ESCAPE_IDENTIFIER_FILE@ ln -s '$file' 'targetFolder/$identifier' && #end for - #end if - #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) #set $targetfileslist = ' '.join([ 'targetFolder/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $targetFiles ]) - #end if @BINARY@ #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': @@ -63,7 +59,7 @@ && rm -rf aggregatedFilesFolder #end if - ]]></command> + ]]> </command> <inputs> <conditional name="tar_input_conditional"> @@ -72,15 +68,14 @@ <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='targetFiles' type="data" format="tar" label="Target files" multiple="false"/> + <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" /> + <param name='targetFiles' type="data" format="tar" label="Target files" multiple="false" /> </when> <when value="interval_input"> - <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> - <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true"/> + <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true" /> + <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true" /> </when> </conditional> - <conditional name="batchmode_conditional"> <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> @@ -88,20 +83,16 @@ <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='targetFilesOrderFile' type="data" format="txt" label="Target file order"/> - + <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" /> + <param name='targetFilesOrderFile' type="data" format="txt" label="Target file order" /> </when> <when value="optionSinglemode"> </when> </conditional> - <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 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="aggregatedFilesCollection" type="list" label="Aggregated files"> - <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" /> </collection> <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${tool.name} aggregated file names"> @@ -113,78 +104,73 @@ </outputs> <tests> <test> - <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/> - <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt"/> + <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" /> + <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" /> <conditional name="batchmode_conditional"> - <param name="batchmode_selector" value='optionBatchmode'/> - <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> - <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/> + <param name="batchmode_selector" value='optionBatchmode' /> + <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> + <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' /> </conditional> <output_collection name="aggregatedFilesCollection" type="list" count="6"> - <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/> - <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/> - - <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4"/> - <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4"/> - - <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4"/> - <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4"/> + <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4" /> + <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4" /> + <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4" /> + <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt" ftype="interval" lines_diff="4" /> + <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4" /> + <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" file="cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt" ftype="interval" lines_diff="4" /> </output_collection> - - <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/> + <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" /> </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"/> - <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt"/> + <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="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" /> <conditional name="batchmode_conditional"> - <param name="batchmode_selector" value='optionSinglemode'/> + <param name="batchmode_selector" value='optionSinglemode' /> </conditional> <output_collection name="aggregatedFilesCollection" type="list" count="2"> - <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/> - <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/> + <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4" /> + <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.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_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/> - <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.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/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" /> + <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.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="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/> + <param name="batchmode_selector" value='optionBatchmode' /> + <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> + <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' /> </conditional> - - <param name='tar' value='True'/> - + <param name='tar' value='True' /> <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' /> - <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/> + <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" /> </test> - <test> + <test> <conditional name="tar_input_conditional"> - <param name="tar_input_selector" value='tar_input'/> - <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar"/> - <param name="targetFiles" value="cHi-C/chicSignificantInteractions/targetFolder.tar"/> + <param name="tar_input_selector" value='tar_input' /> + <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar" /> + <param name="targetFiles" value="cHi-C/chicSignificantInteractions/targetFolder.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="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/> + <param name="batchmode_selector" value='optionBatchmode' /> + <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> + <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt' /> </conditional> - <param name='tar' value='True'/> + <param name='tar' value='True' /> <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' /> - <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/> + <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" /> </test> </tests> <help><![CDATA[ @@ -199,6 +185,6 @@ 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>