Mercurial > repos > iuc > schicexplorer_schicnormalize

diff scHicNormalize.xml @ 1:7c2387e72aac draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
author iuc
date Tue, 10 Mar 2020 15:14:00 -0400
parents 6eda3d3b562d
children 66e96c3d3c5d
line wrap: on
line diff
--- a/scHicNormalize.xml	Thu Jan 23 16:09:58 2020 -0500
+++ b/scHicNormalize.xml	Tue Mar 10 15:14:00 2020 -0400
@@ -8,9 +8,9 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix '$matrix_mcooler'
+        --matrix '$matrix_scooler'
 
-        --outFileName normalized_matrix.mcool
+        --outFileName normalized_matrix.scool
 
         --threads @THREADS@
 
@@ -19,15 +19,15 @@
     ]]></command>
     <inputs>
         
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="normalized_matrix.mcool" format="mcool" label="${tool.name} on ${on_string}: normalized matrix"/>
+        <data name="outFileName" from_work_dir="normalized_matrix.scool" format="scool" label="${tool.name} on ${on_string}: normalized 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, 
@@ -188,7 +188,9 @@
 Normalize matrices
 ==================
 
-scHicNOrmalize normalizes all read coverages to the lowest read coverage found in a mcool file.
+scHicNormalize scales the read coverage of all matrices stored in the provided scool file to the matrix displaying the lowest read coverage in the said file.
+This is a highly parallelized version of HiCExplorer's ̀ hicNormalize`, for more information, you can refer to this page:
+https://hicexplorer.readthedocs.io/en/latest/content/tools/hicNormalize.html
 
 For more information about scHiCExplorer please consider our documentation on readthedocs.io_