Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

diff hicCorrectMatrix.xml @ 15:c543c41377dd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 06:53:35 -0400
parents 1e622e371512
children e4cb7809df61
line wrap: on
line diff
--- a/hicCorrectMatrix.xml	Wed Feb 05 19:39:47 2020 -0500
+++ b/hicCorrectMatrix.xml	Wed Mar 11 06:53:35 2020 -0400
@@ -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