Mercurial > repos > iuc > schicexplorer_schicadjustmatrix
changeset 1:799a9fe1265c 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 16:09:03 2020 -0500 +++ b/macros.xml Tue Mar 10 15:13:23 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/scHicAdjustMatrix.xml Thu Jan 23 16:09:03 2020 -0500 +++ b/scHicAdjustMatrix.xml Tue Mar 10 15:13:23 2020 -0400 @@ -8,7 +8,7 @@ <command detect_errors="exit_code"><![CDATA[ @BINARY@ - --matrix '$matrix_mcooler' + --matrix '$matrix_scooler' --action $action_selector #if $chromosomes: #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) @@ -16,7 +16,7 @@ #end if - --outFileName adjusted_matrix.mcool + --outFileName adjusted_matrix.scool --threads @THREADS@ @@ -25,7 +25,7 @@ ]]></command> <inputs> - <expand macro="matrix_mcooler_macro"/> + <expand macro="matrix_scooler_macro"/> <param name="action_selector" type="select" label="Action to take apply on matrices:"> <option value="keep" selected="True">Keep the listed chromosomes</option> <option value="remove" >Remove the listed chromosomes</option> @@ -33,14 +33,14 @@ <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> </inputs> <outputs> - <data name="outFileName" from_work_dir="adjusted_matrix.mcool" format="mcool" label="${tool.name} on ${on_string}: merged matrix"/> + <data name="outFileName" from_work_dir="adjusted_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Adjusted matrix"/> </outputs> <tests> <test> - <param name='matrix_mcooler' value='test_matrix.mcool' /> + <param name='matrix_scooler' value='test_matrix.scool' /> <param name='clusterMethod_selector' value='keep' /> <param name='chromosomes' value='chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX' /> - <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, @@ -201,7 +201,7 @@ Adjust all matrices =================== -scHicAdjustMatrix is a tool to keep or remove a list of chromosomes of all Hi-C matrices stored in the mcool file. +scHicAdjustMatrix is a tool to keep or remove a list of chromosomes of all Hi-C matrices stored in the scool file. For more information about scHiCExplorer please consider our documentation on readthedocs.io_
--- a/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 16:09:03 2020 -0500 +++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:13:23 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