Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

diff hicCorrectMatrix.xml @ 18:77276abe70c5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Tue, 10 Mar 2020 18:59:56 +0000
parents 14edfcba0e3a
children 1a238d3b7b33
line wrap: on
line diff
--- a/hicCorrectMatrix.xml	Thu Feb 06 00:23:59 2020 +0000
+++ b/hicCorrectMatrix.xml	Tue Mar 10 18:59:56 2020 +0000
@@ -7,7 +7,7 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
-        
+
         @BINARY@
             $mode.mode_selector
             --matrix 'matrix.$matrix_h5_cooler.ext'
@@ -22,7 +22,7 @@
                 #if $mode.correctionMethod.correctionMethod_selector == 'ice':
                     --correctionMethod ICE
                     --iterNum $mode.correctionMethod.iterNum
-                    
+
 
                     #if $mode.correctionMethod.filterThreshold_low and $mode.correctionMethod.filterThreshold_large:
                         --filterThreshold $mode.correctionMethod.filterThreshold_low $mode.correctionMethod.filterThreshold_large
@@ -157,7 +157,7 @@
 
             <param name="mode_selector" value="correct"/>
             <param name='correctionMethod_selector' value='kr'/>
-            
+
             <output name="outFileName" ftype="h5">
                 <assert_contents>
                     <has_h5_keys keys='correction_factors,intervals,matrix'/>
@@ -169,7 +169,7 @@
 
             <param name="mode_selector" value="correct"/>
             <param name='correctionMethod_selector' value='kr'/>
-            
+
             <output name="outFileName" ftype="cool">
                 <assert_contents>
                     <has_h5_keys keys='bins,chroms,indexes,pixels'/>
@@ -254,7 +254,7 @@
 Also, low scoring bins can be caused by absence of a restriction site in the bin or because the restriction
 site is present but the restriction enzyme did not cut. The valley between the two peaks in the
 histogram is set by default as cutoff threshold.
-However, it is important to revise this as in some cases the selected value could not be correct. 
+However, it is important to revise this as in some cases the selected value could not be correct.
 
 
 .. image:: $PATH_TO_IMAGES/diagnostic_plot.png