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Changeset 1:259899fbb6ae (2020-03-10)

Previous changeset 0:1a1e085c352e (2020-01-23) Next changeset 2:95b1216e1e70 (2023-04-14)

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

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

diff -r 1a1e085c352e -r 259899fbb6ae macros.xml
--- a/macros.xml Thu Jan 23 16:02:12 2020 -0500
+++ b/macros.xml Tue Mar 10 15:09:29 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 1a1e085c352e -r 259899fbb6ae scHicPlotConsensusMatrices.xml
--- a/scHicPlotConsensusMatrices.xml Thu Jan 23 16:02:12 2020 -0500
+++ b/scHicPlotConsensusMatrices.xml Tue Mar 10 15:09:29 2020 -0400

[

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

-        --matrix $matrix_mcooler
+        --matrix $matrix_scooler
         #if $chromosomes:
             #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
             --chromosomes $chromosome
@@ -28,7 +28,7 @@

     ]]></command>
     <inputs>
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
         <expand macro="colormap" />
         <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
@@ -41,7 +41,7 @@

     </inputs>
     <outputs>
-        <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
+        <data name='output_plot' from_work_dir='plot' format='png' label='Consensus matrix plot on ${on_string}'>
             <change_format>
                 <when input="image_file_format" value="svg" format="svg" />
                 <when input="image_file_format" value="pdf" format="pdf" />
@@ -50,13 +50,13 @@
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' />
+            <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' />
             <param name="image_file_format" value="png" />
             <param name="dpi" value="300" />
             <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/>
         </test>
          <test>
-            <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' />
+            <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' />
             <param name="image_file_format" value="png" />
             <param name="dpi" value="300" />
             <param name="chromosomes" value="chr1 chr2" />
@@ -70,7 +70,7 @@
Plot consensus matrices
=======================

-scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster.
+scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster. This tool is useful to compare the single cell clusters.

.. image:: $PATH_TO_IMAGES/consensus_svl_spectral.png
    :width: 50%

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diff -r 1a1e085c352e -r 259899fbb6ae test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 16:02:12 2020 -0500
+++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:09:29 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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