Galaxy |

Changeset 1:09f8be8a6e76 (2020-03-10)

Previous changeset 0:35c211c5146d (2020-01-23) Next changeset 2:41b415c410e3 (2023-04-14)

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

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

diff -r 35c211c5146d -r 09f8be8a6e76 macros.xml
--- a/macros.xml Thu Jan 23 16:02:54 2020 -0500
+++ b/macros.xml Tue Mar 10 15:10:08 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 35c211c5146d -r 09f8be8a6e76 scHicInfo.xml
--- a/scHicInfo.xml Thu Jan 23 16:02:54 2020 -0500
+++ b/scHicInfo.xml Tue Mar 10 15:10:08 2020 -0400

[

@@ -1,27 +1,24 @@
<tool id="schicexplorer_schicinfo" name="@BINARY@" version="@WRAPPER_VERSION@.0">
-    <description>information about a single-cell mcool matrix</description>
+    <description>information about a single-cell scool matrix</description>
     <macros>
         <token name="@BINARY@">scHicInfo</token>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command detect_errors="exit_code"><![CDATA[
-    #import re
-        #set mcoolFile = @ESCAPE_IDENTIFIER_MCOOL@
-        ln -s '$matrix_mcooler' '$mcoolFile' &&
+    <command detect_errors="exit_code"><![CDATA[
         @BINARY@
-        --matrix $mcoolFile
+        --matrix '$matrix_scooler'
         >> matrices_info.txt
     ]]></command>
     <inputs>
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
    </inputs>
     <outputs>
         <data name="outFileName" from_work_dir="matrices_info.txt" format="txt" label="${tool.name} on ${on_string}: Matrix Info"/>
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <output name="outFileName" file="scHicInfo/matrices_info.txt" ftype="txt" compare="sim_size" delta="4000"/>
         </test>
     </tests>
@@ -30,11 +27,11 @@
Consensus matrices
==================

-scHicInfo gives information about the single-cell Hi-C mcool file. For example:
+scHicInfo gives information about the provided single-cell Hi-C scool file. For example:

.. code-block::

-    Filename: nagano2017_raw.mcool
+    Filename: nagano2017_raw.scool
     Contains 3882 single-cell matrices
     The information stored via cooler.info of the first cell is:

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diff -r 35c211c5146d -r 09f8be8a6e76 test-data/scHicQualityControl/qc_report.txt
--- a/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 16:02:54 2020 -0500
+++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:10:08 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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