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Changeset 1:eeb26f378f34 (2020-03-10)

Previous changeset 0:7cbd84a1f985 (2020-01-23) Next changeset 2:e6ec3914a076 (2023-04-14)

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

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

diff -r 7cbd84a1f985 -r eeb26f378f34 macros.xml
--- a/macros.xml Thu Jan 23 16:01:20 2020 -0500
+++ b/macros.xml Tue Mar 10 15:08:53 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 7cbd84a1f985 -r eeb26f378f34 scHicClusterSVL.xml
--- a/scHicClusterSVL.xml Thu Jan 23 16:01:20 2020 -0500
+++ b/scHicClusterSVL.xml Tue Mar 10 15:08:53 2020 -0400

[

@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@

-        --matrix '$matrix_mcooler'
+        --matrix '$matrix_scooler'

         --numberOfClusters $numberOfClusters
         --distanceShortRange $distanceShortRange
@@ -27,7 +27,7 @@
     ]]></command>
     <inputs>

-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name="clusterMethod_selector" type="select" label="Cluster method:">
                 <option value="kmeans" selected="True">K-means</option>
                 <option value="spectral" >Spectral clustering</option>
@@ -44,7 +44,7 @@
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='kmeans' />
             <param name='numberOfClusters' value='3' />
             <param name='distanceShortRange' value='2000000' />
@@ -54,7 +54,7 @@
         </test>

         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='spectral' />
             <param name='numberOfClusters' value='3' />
             <param name='distanceShortRange' value='2000000' />
@@ -71,7 +71,7 @@

scHicClusterSVL uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle.
The clustering is applied on dimension reduced data based on the ratio of short vs long range contacts per chromosome. This approach reduces the number of dimensions from samples * (number of bins)^2 to samples * (number of chromosomes).
-Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite. They can give you better results,
+Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite such as `scHicCluster`, `scHicClusterMinHash` and `scHicClusterSVL`. They can give you better results,
can be faster or less memory demanding.

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

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diff -r 7cbd84a1f985 -r eeb26f378f34 test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 16:01:20 2020 -0500
+++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:08:53 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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