| Previous changeset 3:8fb584526458 (2020-03-24) Next changeset 5:889194374660 (2020-12-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e" |
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modified:
chicViewpoint.xml test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png test-data/cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png |
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added:
test-data/cHi-C/chicAggregateStatistic/batch_mode.tar test-data/cHi-C/chicDifferentialTest/batch_mode_chi2.tar test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile.tar test-data/cHi-C/chicPlotViewpoint/batchMode/plots.tar test-data/cHi-C/chicSignificantInteractions/significantFilesFolder.tar test-data/cHi-C/chicSignificantInteractions/targetFolder.tar test-data/cHi-C/chicViewpoint/output_1.tar test-data/cHi-C/chicViewpoint/viewpoints.tar |
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| diff -r 8fb584526458 -r 78b70d78a596 chicViewpoint.xml --- a/chicViewpoint.xml Tue Mar 24 14:32:20 2020 -0400 +++ b/chicViewpoint.xml Fri Aug 14 06:12:45 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1"> <description>computes viewpoints with the given reference points and a background model.</description> <macros> <token name="@BINARY@">chicViewpoint</token> @@ -27,6 +27,13 @@ --backgroundModelFile '$backgroundModelFile' --outputFolder interactionFiles $writeFileNamesToFile + + #if $tar: + && cd interactionFiles + && tar -cvf ../viewpoints.tar . + && cd .. + && rm -rf interactionFiles + #end if ]]></command> <inputs> @@ -47,6 +54,9 @@ <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)" help="Set this parameter if you want to use the batch processing mode for the further analysis."/> + <param name='tar' type='boolean' checked="false" label="tar output to one file" + help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/> + </inputs> <outputs> <collection name="interactionFilesCollection" type="list" label="Interaction files"> @@ -55,6 +65,9 @@ <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names"> <filter>writeFileNamesToFile</filter> </data> + <data name="interactionFilesTar" from_work_dir="viewpoints.tar" format="tar" label="${tool.name} interaction file names tar"> + <filter>tar</filter> + </data> </outputs> <tests> <test> @@ -103,6 +116,21 @@ <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> --> </test> + <test> + <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> + + <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/> + <param name="backgroundModelFile" value="cHi-C/background.txt"/> + <param name="fixateRange" value="500000"/> + <param name="rangeUpstream" value="200000"/> + <param name="rangeDownstream" value="200000"/> + <param name="writeFileNamesToFile" value="True"/> + <param name='tar' value='True'/> + + <output name="interactionFilesTar" file="cHi-C/chicViewpoint/viewpoints.tar" ftype='tar' compare="sim_size" delta='40000' /> + <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> + + </test> </tests> <help><
