Mercurial > repos > iuc > schicexplorer_schicnormalize
changeset 1:7c2387e72aac draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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--- a/macros.xml Thu Jan 23 16:09:58 2020 -0500 +++ b/macros.xml Tue Mar 10 15:14:00 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/scHicNormalize.xml Thu Jan 23 16:09:58 2020 -0500 +++ b/scHicNormalize.xml Tue Mar 10 15:14:00 2020 -0400 @@ -8,9 +8,9 @@ <command detect_errors="exit_code"><![CDATA[ @BINARY@ - --matrix '$matrix_mcooler' + --matrix '$matrix_scooler' - --outFileName normalized_matrix.mcool + --outFileName normalized_matrix.scool --threads @THREADS@ @@ -19,15 +19,15 @@ ]]></command> <inputs> - <expand macro="matrix_mcooler_macro"/> + <expand macro="matrix_scooler_macro"/> </inputs> <outputs> - <data name="outFileName" from_work_dir="normalized_matrix.mcool" format="mcool" label="${tool.name} on ${on_string}: normalized matrix"/> + <data name="outFileName" from_work_dir="normalized_matrix.scool" format="scool" label="${tool.name} on ${on_string}: normalized matrix"/> </outputs> <tests> <test> - <param name='matrix_mcooler' value='test_matrix.mcool' /> - <output name="outFileName" ftype="mcool"> + <param name='matrix_scooler' value='test_matrix.scool' /> + <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, @@ -188,7 +188,9 @@ Normalize matrices ================== -scHicNOrmalize normalizes all read coverages to the lowest read coverage found in a mcool file. +scHicNormalize scales the read coverage of all matrices stored in the provided scool file to the matrix displaying the lowest read coverage in the said file. +This is a highly parallelized version of HiCExplorer's ̀ hicNormalize`, for more information, you can refer to this page: +https://hicexplorer.readthedocs.io/en/latest/content/tools/hicNormalize.html For more information about scHiCExplorer please consider our documentation on readthedocs.io_
--- a/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 16:09:58 2020 -0500 +++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:14:00 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