Mercurial > repos > iuc > schicexplorer_schicinfo
changeset 1:09f8be8a6e76 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 16:02:54 2020 -0500 +++ b/macros.xml Tue Mar 10 15:10:08 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/scHicInfo.xml Thu Jan 23 16:02:54 2020 -0500 +++ b/scHicInfo.xml Tue Mar 10 15:10:08 2020 -0400 @@ -1,27 +1,24 @@ <tool id="schicexplorer_schicinfo" name="@BINARY@" version="@WRAPPER_VERSION@.0"> - <description>information about a single-cell mcool matrix</description> + <description>information about a single-cell scool matrix</description> <macros> <token name="@BINARY@">scHicInfo</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ - #import re - #set mcoolFile = @ESCAPE_IDENTIFIER_MCOOL@ - ln -s '$matrix_mcooler' '$mcoolFile' && + <command detect_errors="exit_code"><![CDATA[ @BINARY@ - --matrix $mcoolFile + --matrix '$matrix_scooler' >> matrices_info.txt ]]></command> <inputs> - <expand macro="matrix_mcooler_macro"/> + <expand macro="matrix_scooler_macro"/> </inputs> <outputs> <data name="outFileName" from_work_dir="matrices_info.txt" format="txt" label="${tool.name} on ${on_string}: Matrix Info"/> </outputs> <tests> <test> - <param name='matrix_mcooler' value='test_matrix.mcool' /> + <param name='matrix_scooler' value='test_matrix.scool' /> <output name="outFileName" file="scHicInfo/matrices_info.txt" ftype="txt" compare="sim_size" delta="4000"/> </test> </tests> @@ -30,11 +27,11 @@ Consensus matrices ================== -scHicInfo gives information about the single-cell Hi-C mcool file. For example: +scHicInfo gives information about the provided single-cell Hi-C scool file. For example: .. code-block:: - Filename: nagano2017_raw.mcool + Filename: nagano2017_raw.scool Contains 3882 single-cell matrices The information stored via cooler.info of the first cell is:
--- a/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 16:02:54 2020 -0500 +++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:10:08 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