Galaxy |

Changeset 1:5f2eacae0bb8 (2020-03-10)

Previous changeset 0:061a8c076eb1 (2020-01-23) Next changeset 2:4a841ab67e3b (2023-04-14)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"

modified:
macros.xml
scHicQualityControl.xml
test-data/scHicQualityControl/coverage.png
test-data/scHicQualityControl/density.png
test-data/scHicQualityControl/qc_report.txt

diff -r 061a8c076eb1 -r 5f2eacae0bb8 macros.xml
--- a/macros.xml Thu Jan 23 16:10:53 2020 -0500
+++ b/macros.xml Tue Mar 10 15:15:17 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">

diff -r 061a8c076eb1 -r 5f2eacae0bb8 scHicQualityControl.xml
--- a/scHicQualityControl.xml Thu Jan 23 16:10:53 2020 -0500
+++ b/scHicQualityControl.xml Tue Mar 10 15:15:17 2020 -0400

[

b'@@ -8,7 +8,7 @@\n <command detect_errors="exit_code"><![CDATA[\n @BINARY@\n \n- --matrix \'$matrix_mcooler\'\n+ --matrix \'$matrix_scooler\'\n #if $chromosomes:\n #set $chromosome = \' \'.join([ \'\\\'%s\\\'\' % $chrom for $chrom in str($chromosomes).split(\' \') ])\n --chromosomes $chromosome\n@@ -22,7 +22,7 @@\n --outFileNameDensity plot_density.$image_file_format\n --outFileNameReadCoverage plot_read_coverage.$image_file_format\n --outFileNameQCReport report.txt\n- --outputMcool filtered_matrices.mcool\n+ --outputScool filtered_matrices.scool\n \n --threads @THREADS@\n \n@@ -32,7 +32,7 @@\n \n ]]></command>\n <inputs>\n- <expand macro="matrix_mcooler_macro"/>\n+ <expand macro="matrix_scooler_macro"/>\n <param name="minimumReadCoverage" type="integer" value="1000000" label="Minimum read coverage" help=\'Remove all samples with a lower read coverage as this value.\' /> \n <param name="minimumDensity" type="float" value="0.001" label="Minimum density" help=\'Remove all samples with a lower density as this value.\' /> \n <param name="maximumRegionToConsider" type="integer" value="30000000" label="Maximum region to consider" help=\'To compute the density, consider only this genomic distance around the diagonal.\' /> \n@@ -58,12 +58,12 @@\n </change_format>\n </data>\n <data name="report" from_work_dir="report.txt" format="txt" label="${tool.name} on ${on_string}: QC report"/>\n- <data name="outFileName" from_work_dir="filtered_matrices.mcool" format="mcool" label="${tool.name} on ${on_string}: Filtered matrices"/>\n+ <data name="outFileName" from_work_dir="filtered_matrices.scool" format="scool" label="${tool.name} on ${on_string}: Filtered matrices"/>\n \n </outputs>\n <tests>\n <test>\n- <param name=\'matrix_mcooler\' value=\'test_matrix.mcool\' />\n+ <param name=\'matrix_scooler\' value=\'test_matrix.scool\' />\n <param name=\'minimumReadCoverage\' value=\'100000\' />\n <param name=\'minimumDensity\' value=\'0.001\' />\n <param name=\'maximumRegionToConsider\' value=\'30000000\' />\n@@ -72,11 +72,81 @@\n <output name="output_plot_density" file="scHicQualityControl/density.png" ftype="png" compare="sim_size" delta="35000"/> \n <output name="output_plot_read_coverage" file="scHicQualityControl/coverage.png" ftype="png" compare="sim_size" delta="35000"/> \n <output name="report" file="scHicQualityControl/qc_report.txt" ftype="txt" compare="sim_size" delta="35000"/> \n- <output name="outFileName" ftype="mcool">\n+ <output name="outFileName" ftype="scool">\n <assert_contents>\n- <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, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes/bin1_offset, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes/chrom_offset, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels/bin1_id, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels/bin2_id, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels/count, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/bins, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/bins/end, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/chroms, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/chroms/name, Diploid_1_CGTACTAG'..b"GGCGA_AAGGAGTA_R1fastqgz/pixels, \n+ Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/pixels/bin1_id, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/pixels/bin2_id,\n+ Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/pixels/count, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz, \n+ Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins/chrom,\n+ Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins/end, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins/start,\n+ Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms/length, \n+ Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms/name, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes, \n+ Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/bin1_offset, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/chrom_offset, \n+ Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin1_id, \n+ Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin2_id, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/count,\n+ Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins, \n+ Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/chrom, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/end,\n+ Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/start, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms,\n+ Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms/length, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms/name,\n+ Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/bin1_offset, \n+ Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/chrom_offset, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels,\n+ Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin1_id, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin2_id, \n+ Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/count, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz,\n+ Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/chrom, \n+ Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/end, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/start,\n+ Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/length, \n+ Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/name, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes,\n+ Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/bin1_offset, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/chrom_offset, \n+ Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin1_id, \n+ Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin2_id, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/count'/></assert_contents>\n </output>\n </test>\n </tests>\n@@ -106,7 +176,8 @@\n Number of removed matrices due to too many zero bins (< 0.02 density, within 30000000 relative genomic distance): 610\n 2508 samples passed the quality control. Please consider matrices with a low read coverage may be the matrices with a low density and overlap therefore.\n \n-4. The scHi-C mcool matrix with the filtered matrices.\n+4. The scHi-C scool matrix with the filtered matrices.\n+\n For more information about scHiCExplorer please consider our documentation on readthedocs.io_\n \n .. _readthedocs.io: http://schicexplorer.readthedocs.io/\n"

diff -r 061a8c076eb1 -r 5f2eacae0bb8 test-data/scHicConsensusMatrices/consensus_matrix.mcool

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diff -r 061a8c076eb1 -r 5f2eacae0bb8 test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 16:10:53 2020 -0500
+++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:15:17 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

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