Galaxy |

Changeset 1:ecae4e42d40a (2020-03-10)

Previous changeset 0:18ac7f83ae0e (2020-01-23) Next changeset 2:47ef02546fe9 (2023-04-14)

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

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

diff -r 18ac7f83ae0e -r ecae4e42d40a macros.xml
--- a/macros.xml Thu Jan 23 16:03:51 2020 -0500
+++ b/macros.xml Tue Mar 10 15:10:44 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 18ac7f83ae0e -r ecae4e42d40a scHicMergeMatrixBins.xml
--- a/scHicMergeMatrixBins.xml Thu Jan 23 16:03:51 2020 -0500
+++ b/scHicMergeMatrixBins.xml Tue Mar 10 15:10:44 2020 -0400

[

@@ -8,14 +8,14 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@

-        --matrix '$matrix_mcooler'
+        --matrix '$matrix_scooler'
         --numBins $numberOfBins

         #if $runningWindow:
             $runningWindow
         #end if

-        --outFileName merged_matrices.mcool
+        --outFileName merged_matrices.scool

         --threads @THREADS@

@@ -24,19 +24,19 @@
     ]]></command>
     <inputs>

-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name="numberOfBins" type="integer" value="10"  label="Number of bins to merge" help='Number of bins to merge to achieve the desired resolution. For example: To merge a 10kb matrix to 1MB, 10kb * 100 = 1MB i.e. the value needs to be 100.' />
         <param name='runningWindow' type='boolean' truevalue='--runningWindow' label='Running window' help='Set to merge for using a running window of length --numBins. Must be an odd number.'/>

     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="merged_matrices.mcool" format="mcool" label="${tool.name} on ${on_string}: Adjusted matrix"/>
+        <data name="outFileName" from_work_dir="merged_matrices.scool" format="scool" label="${tool.name} on ${on_string}: Merged matrix"/>
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='numberOfBins' value='10' />
-            <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,
@@ -191,11 +191,11 @@
             </output>
         </test>
        <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='numberOfBins' value='11' />
             <param name='runningWindow' value='true' />

-            <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,
@@ -355,8 +355,12 @@
Change the resolution of the scHi-C matrices
============================================

-Merges bins from a Hi-C matrix. For example, using a matrix containing 5kb bins, a matrix of 50kb bins can be derived using --numBins 10.
-
+**scHicMergeMatrixBins** is used to decrease the resolution of single cell matrices stored in a scool file by merging their adjacent bins. With this tool, you can for example create out of a 5kb
+contact matrix a 50kb one:
+Number of bins to merge = 10
+5kb * 10 = 50k
+Depending on the downstream analyses to perform on single cell Hi-C matrices generated with HiCExplorer, one might need different bin resolutions, for instance during clustering or for plotting small or large regions of consensus matrices.
+The best practice is to merge bins in uncorrected matrices, and correct the lower resolution matrices using `scHicCorrectMatrices` subsequently.

For more information about scHiCExplorer please consider our documentation on readthedocs.io_

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicConsensusMatrices/consensus_matrix.mcool

Binary file test-data/scHicConsensusMatrices/consensus_matrix.mcool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicConsensusMatrices/consensus_matrix.scool

Binary file test-data/scHicConsensusMatrices/consensus_matrix.scool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicCreateBulkMatrix/bulk_matrix.cool

Binary file test-data/scHicCreateBulkMatrix/bulk_matrix.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToMCool/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz.cool

Binary file test-data/scHicMergeToMCool/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicMergeToSCool/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz.cool

Binary file test-data/scHicMergeToSCool/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz.cool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicQualityControl/coverage.png

Binary file test-data/scHicQualityControl/coverage.png has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicQualityControl/density.png

Binary file test-data/scHicQualityControl/density.png has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 16:03:51 2020 -0500
+++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:10:44 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

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/test_matrix.mcool

Binary file test-data/test_matrix.mcool has changed

diff -r 18ac7f83ae0e -r ecae4e42d40a test-data/test_matrix.scool

Binary file test-data/test_matrix.scool has changed