Mercurial > repos > iuc > schicexplorer_schicplotconsensusmatrices
changeset 1:259899fbb6ae 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 16:02:12 2020 -0500 +++ b/macros.xml Tue Mar 10 15:09:29 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/scHicPlotConsensusMatrices.xml Thu Jan 23 16:02:12 2020 -0500 +++ b/scHicPlotConsensusMatrices.xml Tue Mar 10 15:09:29 2020 -0400 @@ -8,7 +8,7 @@ <command detect_errors="exit_code"><![CDATA[ @BINARY@ - --matrix $matrix_mcooler + --matrix $matrix_scooler #if $chromosomes: #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) --chromosomes $chromosome @@ -28,7 +28,7 @@ ]]></command> <inputs> - <expand macro="matrix_mcooler_macro"/> + <expand macro="matrix_scooler_macro"/> <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> <expand macro="colormap" /> <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> @@ -41,7 +41,7 @@ </inputs> <outputs> - <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'> + <data name='output_plot' from_work_dir='plot' format='png' label='Consensus matrix plot on ${on_string}'> <change_format> <when input="image_file_format" value="svg" format="svg" /> <when input="image_file_format" value="pdf" format="pdf" /> @@ -50,13 +50,13 @@ </outputs> <tests> <test> - <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' /> + <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' /> <param name="image_file_format" value="png" /> <param name="dpi" value="300" /> <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/> </test> <test> - <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' /> + <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' /> <param name="image_file_format" value="png" /> <param name="dpi" value="300" /> <param name="chromosomes" value="chr1 chr2" /> @@ -70,7 +70,7 @@ Plot consensus matrices ======================= -scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster. +scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster. This tool is useful to compare the single cell clusters. .. image:: $PATH_TO_IMAGES/consensus_svl_spectral.png :width: 50%
--- a/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 16:02:12 2020 -0500 +++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:09:29 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