Mercurial > repos > iuc > schicexplorer_schicmergematrixbins
changeset 1:ecae4e42d40a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
line wrap: on
line diff
--- a/macros.xml Thu Jan 23 16:03:51 2020 -0500 +++ b/macros.xml Tue Mar 10 15:10:44 2020 -0400 @@ -1,6 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">4</token> <xml name="requirements"> <requirements> @@ -9,8 +9,8 @@ </requirements> <version_command>@BINARY@ --version</version_command> </xml> - <xml name='matrix_mcooler_macro'> - <param name='matrix_mcooler' type="data" format="mcool" + <xml name='matrix_scooler_macro'> + <param name='matrix_scooler' type="data" format="scool" label="Matrix to compute on"/> </xml> <xml name='matrix_cooler_multiple_macro'> @@ -18,7 +18,7 @@ label="Matricies to compute on" multiple="true"/> </xml> <token name="@ESCAPE_IDENTIFIER_FASTQ@"><![CDATA[re.sub('[^\s\w\.]', '_', str($fastq.element_identifier))]]></token> - <token name="@ESCAPE_IDENTIFIER_MCOOL@"><![CDATA[re.sub('[^\s\w\.]', '_', str($matrix_mcooler.element_identifier))]]></token> + <token name="@ESCAPE_IDENTIFIER_SCOOL@"><![CDATA[re.sub('[^\s\w\.]', '_', str($matrix_scooler.element_identifier))]]></token> <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token> <xml name="citations">
--- a/scHicMergeMatrixBins.xml Thu Jan 23 16:03:51 2020 -0500 +++ b/scHicMergeMatrixBins.xml Tue Mar 10 15:10:44 2020 -0400 @@ -8,14 +8,14 @@ <command detect_errors="exit_code"><![CDATA[ @BINARY@ - --matrix '$matrix_mcooler' + --matrix '$matrix_scooler' --numBins $numberOfBins #if $runningWindow: $runningWindow #end if - --outFileName merged_matrices.mcool + --outFileName merged_matrices.scool --threads @THREADS@ @@ -24,19 +24,19 @@ ]]></command> <inputs> - <expand macro="matrix_mcooler_macro"/> + <expand macro="matrix_scooler_macro"/> <param name="numberOfBins" type="integer" value="10" label="Number of bins to merge" help='Number of bins to merge to achieve the desired resolution. For example: To merge a 10kb matrix to 1MB, 10kb * 100 = 1MB i.e. the value needs to be 100.' /> <param name='runningWindow' type='boolean' truevalue='--runningWindow' label='Running window' help='Set to merge for using a running window of length --numBins. Must be an odd number.'/> </inputs> <outputs> - <data name="outFileName" from_work_dir="merged_matrices.mcool" format="mcool" label="${tool.name} on ${on_string}: Adjusted matrix"/> + <data name="outFileName" from_work_dir="merged_matrices.scool" format="scool" label="${tool.name} on ${on_string}: Merged matrix"/> </outputs> <tests> <test> - <param name='matrix_mcooler' value='test_matrix.mcool' /> + <param name='matrix_scooler' value='test_matrix.scool' /> <param name='numberOfBins' value='10' /> - <output name="outFileName" ftype="mcool"> + <output name="outFileName" ftype="scool"> <assert_contents> <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, @@ -191,11 +191,11 @@ </output> </test> <test> - <param name='matrix_mcooler' value='test_matrix.mcool' /> + <param name='matrix_scooler' value='test_matrix.scool' /> <param name='numberOfBins' value='11' /> <param name='runningWindow' value='true' /> - <output name="outFileName" ftype="mcool"> + <output name="outFileName" ftype="scool"> <assert_contents> <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, @@ -355,8 +355,12 @@ Change the resolution of the scHi-C matrices ============================================ -Merges bins from a Hi-C matrix. For example, using a matrix containing 5kb bins, a matrix of 50kb bins can be derived using --numBins 10. - +**scHicMergeMatrixBins** is used to decrease the resolution of single cell matrices stored in a scool file by merging their adjacent bins. With this tool, you can for example create out of a 5kb +contact matrix a 50kb one: +Number of bins to merge = 10 +5kb * 10 = 50k +Depending on the downstream analyses to perform on single cell Hi-C matrices generated with HiCExplorer, one might need different bin resolutions, for instance during clustering or for plotting small or large regions of consensus matrices. +The best practice is to merge bins in uncorrected matrices, and correct the lower resolution matrices using `scHicCorrectMatrices` subsequently. For more information about scHiCExplorer please consider our documentation on readthedocs.io_
--- a/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 16:03:51 2020 -0500 +++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:10:44 2020 -0400 @@ -1,6 +1,6 @@ -# QC report for single-cell Hi-C data generated by scHiCExplorer 1-dev +# QC report for single-cell Hi-C data generated by scHiCExplorer 4 scHi-C sample contained 20 cells: Number of removed matrices containing bad chromosomes 0 -Number of removed matrices due to low read coverage (< 100000): 8 +Number of removed matrices due to low read coverage (< 100000): 10 Number of removed matrices due to too many zero bins (< 0.001 density, within 30000000 relative genomic distance): 0 -12 samples passed the quality control. Please consider matrices with a low read coverage may be the matrices with a low density and overlap therefore. \ No newline at end of file +10 samples passed the quality control. Please consider matrices with a low read coverage may be the matrices with a low density and overlap therefore. \ No newline at end of file