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Changeset 1:18bdb745b787 (2020-03-10)

Previous changeset 0:49e3fe550e7e (2020-01-23) Next changeset 2:33b1c99cc709 (2023-04-14)

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

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

diff -r 49e3fe550e7e -r 18bdb745b787 macros.xml
--- a/macros.xml Thu Jan 23 15:58:55 2020 -0500
+++ b/macros.xml Tue Mar 10 15:06:59 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 49e3fe550e7e -r 18bdb745b787 scHicConsensusMatrices.xml
--- a/scHicConsensusMatrices.xml Thu Jan 23 15:58:55 2020 -0500
+++ b/scHicConsensusMatrices.xml Tue Mar 10 15:06:59 2020 -0400

[

@@ -8,10 +8,10 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@

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

-        --outFileName consensus_matrix.mcool
+        --outFileName consensus_matrix.scool

         --threads @THREADS@

@@ -20,19 +20,19 @@
     ]]></command>
     <inputs>

-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/>

         <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="consensus_matrix.mcool" format="mcool" label="${tool.name} on ${on_string}: Consensus matrices"/>
+        <data name="outFileName" from_work_dir="consensus_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Consensus matrices"/>
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusters' value='scHicConsensusMatrices/cluster_kmeans.txt' />
-            <output name="outFileName" ftype="mcool">
+            <output name="outFileName" ftype="scool">
                 <assert_contents>
                     <has_h5_keys keys='consensus_matrix_cluster_0,
                                         consensus_matrix_cluster_0/bins, consensus_matrix_cluster_0/bins/chrom,
@@ -63,7 +63,8 @@
Consensus matrices
==================

-scHicConsensusMatrices creates based on the clustered samples one consensus matrix for each cluster. The consensus matrices are normalized to an equal read coverage level and are stored all in one mcool matrix.
+scHicConsensusMatrices creates one consensus matrix for each cluster based on the clustered samples. The consensus matrices are normalized to an equal read coverage level and are all stored in one s
+cool file.

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

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diff -r 49e3fe550e7e -r 18bdb745b787 test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 15:58:55 2020 -0500
+++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:06:59 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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