Mercurial > repos > iuc > schicexplorer_schiccorrectmatrices

diff scHicCorrectMatrices.xml @ 1:16dda99bd733 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 15:14:37 -0400
parents 104bedd292cd
children 295558e266d0
line wrap: on
line diff
--- a/scHicCorrectMatrices.xml	Wed Jan 29 17:07:16 2020 -0500
+++ b/scHicCorrectMatrices.xml	Tue Mar 10 15:14:37 2020 -0400
@@ -7,20 +7,20 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
-        --matrix '$matrix_mcooler'
-        --outFileName corrected.mcool
+        --matrix '$matrix_scooler'
+        --outFileName corrected.scool
         --threads @THREADS@
     ]]></command>
     <inputs>
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="corrected.mcool" format="mcool" label="${tool.name} on ${on_string}: KR corrected matrix"/>
+        <data name="outFileName" from_work_dir="corrected.scool" format="scool" label="${tool.name} on ${on_string}: KR corrected 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, 
@@ -180,7 +180,8 @@
 Correct all matrices
 ====================
 
-scHicCorrectmatrices is a tool to correct with HiCExplorer's KR algorithm all Hi-C matrices stored in the mcool file.
+scHicCorrectmatrices is a tool to correct all Hi-C matrices stored in the provided scool file using HiCExplorer's KR algorithm, which is detailed here:
+https://hicexplorer.readthedocs.io/en/latest/content/tools/hicCorrectMatrix.html
 
 For more information about scHiCExplorer please consider our documentation on readthedocs.io_