Mercurial > repos > iuc > schicexplorer_schicplotclusterprofiles
changeset 1:9da580a74230 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 16:07:58 2020 -0500 +++ b/macros.xml Tue Mar 10 15:12:42 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/scHicPlotClusterProfiles.xml Thu Jan 23 16:07:58 2020 -0500 +++ b/scHicPlotClusterProfiles.xml Tue Mar 10 15:12:42 2020 -0400 @@ -8,7 +8,7 @@ <command detect_errors="exit_code"><![CDATA[ @BINARY@ - --matrix $matrix_mcooler + --matrix $matrix_scooler --clusters $clusters #if $chromosomes: #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) @@ -33,7 +33,7 @@ ]]></command> <inputs> - <expand macro="matrix_mcooler_macro"/> + <expand macro="matrix_scooler_macro"/> <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/> <param name="maximalDistance" type="integer" value="2000000" label="Maximal distance" help='Maximal distance to consider for plotting' /> <conditional name="order_by_conditional"> @@ -59,7 +59,7 @@ </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='Cluster profile plot on ${on_string} '> <change_format> <when input="image_file_format" value="svg" format="svg" /> <when input="image_file_format" value="pdf" format="pdf" /> @@ -68,7 +68,7 @@ </outputs> <tests> <test> - <param name='matrix_mcooler' value='test_matrix.mcool' /> + <param name='matrix_scooler' value='test_matrix.scool' /> <param name='clusters' value='scHicPlotClusterProfiles/cluster_kmeans.txt' /> <conditional name="order_by_conditional"> <param name="order_by_selection" value="svl"/> @@ -88,7 +88,8 @@ Plot cluster profiles ===================== -scHicPlotClusterProfiles plots the profile of each scHi-C interaction matrix assoziated to a cluster, within the cluster the matrices can be order either via their short vs long range ratio or by the order of the file. +scHicPlotClusterProfiles plots the profile of each scHi-C interaction matrix associated to a cluster, within the cluster the matrices can be ordered either via their short vs long range ratio or by the order of the file. +This tool is useful as a quality control of a cluster to check if all matrices assigned to that cluster are displaying similar contacts distribution. .. image:: $PATH_TO_IMAGES/clusters_svl_spectral.png :width: 50%
--- a/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 16:07:58 2020 -0500 +++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:12:42 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