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Changeset 1:16dda99bd733 (2020-03-10)

Previous changeset 0:104bedd292cd (2020-01-29) Next changeset 2:295558e266d0 (2023-04-14)

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

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

diff -r 104bedd292cd -r 16dda99bd733 macros.xml
--- a/macros.xml Wed Jan 29 17:07:16 2020 -0500
+++ b/macros.xml Tue Mar 10 15:14:37 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 104bedd292cd -r 16dda99bd733 scHicCorrectMatrices.xml
--- a/scHicCorrectMatrices.xml Wed Jan 29 17:07:16 2020 -0500
+++ b/scHicCorrectMatrices.xml Tue Mar 10 15:14:37 2020 -0400

[

@@ -7,20 +7,20 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
-        --matrix '$matrix_mcooler'
-        --outFileName corrected.mcool
+        --matrix '$matrix_scooler'
+        --outFileName corrected.scool
         --threads @THREADS@
     ]]></command>
     <inputs>
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="corrected.mcool" format="mcool" label="${tool.name} on ${on_string}: KR corrected matrix"/>
+        <data name="outFileName" from_work_dir="corrected.scool" format="scool" label="${tool.name} on ${on_string}: KR corrected matrix"/>
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
-            <output name="outFileName" ftype="mcool">
+            <param name='matrix_scooler' value='test_matrix.scool' />
+            <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,
@@ -180,7 +180,8 @@
Correct all matrices
====================

-scHicCorrectmatrices is a tool to correct with HiCExplorer's KR algorithm all Hi-C matrices stored in the mcool file.
+scHicCorrectmatrices is a tool to correct all Hi-C matrices stored in the provided scool file using HiCExplorer's KR algorithm, which is detailed here:
+https://hicexplorer.readthedocs.io/en/latest/content/tools/hicCorrectMatrix.html

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

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diff -r 104bedd292cd -r 16dda99bd733 test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt Wed Jan 29 17:07:16 2020 -0500
+++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:14:37 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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