diff unionBedGraphs.xml @ 26:c0fbce5dc84a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:20 -0400
parents a2d4c30ba2f9
children b0d5e752c0c5
line wrap: on
line diff
--- a/unionBedGraphs.xml	Wed Sep 14 17:29:56 2016 -0400
+++ b/unionBedGraphs.xml	Mon Oct 17 10:13:20 2016 -0400
@@ -105,9 +105,6 @@
 
 This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.
 
-.. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/ubg.png
-
-
 .. class:: warningmark
 
 This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file).
@@ -135,7 +132,7 @@
 **Examples using the Zero Coverage checkbox**
 
 Output example (*without* checking "Report regions with zero coverage")::
-    
+
     chr1     900    1000     0    60     0
     chr1    1000    1500    10    60     0
     chr1    1500    1600     0    60     0
@@ -148,7 +145,7 @@
 
 
 Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).::
-    
+
     chr1       0          900     0     0     0 (*)
     chr1     900         1000     0    60     0
     chr1    1000         1500    10    60     0
@@ -160,7 +157,7 @@
     chr1    2050         2070    20     0    80
     chr1    2070         2090    20     0     0
     chr1    2090         2100    20     0    20
-    chr1    2100    247249719     0     0     0 (*) 
+    chr1    2100    247249719     0     0     0 (*)
 
 
 ------
@@ -170,7 +167,7 @@
 The default value is '0', but you can use any other value.
 
 Output example with **filler = N/A**::
-    
+
     chr1     900    1000    N/A     60    N/A
     chr1    1000    1500     10     60    N/A
     chr1    1500    1600    N/A     60    N/A
@@ -207,14 +204,14 @@
 The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value.
 
 Input Example::
-        
-    File-1                           File-2 
+
+    File-1                           File-2
     chr1   200   300   Sample1       chr1   100   240   0.75
     chr1   400   450   Sample1       chr1   250   700   0.43
     chr1   530   600   Sample2
 
 Output Example::
-    
+
     chr1   100    200    0         0.75
     chr1   200    240    Sample1   0.75
     chr1   240    250    Sample1   0