Mercurial > repos > greg > cwpair2

changeset 12:79a10fe09b66 draft default tip

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Uploaded
author greg
date Wed, 16 Dec 2015 19:41:57 -0500
parents 6383cae47688
children
files cwpair2.xml
diffstat 1 files changed, 11 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/cwpair2.xml	Wed Dec 16 14:18:28 2015 -0500
+++ b/cwpair2.xml	Wed Dec 16 19:41:57 2015 -0500
@@ -156,6 +156,17 @@
 
 -----
 
+**Options**
+
+ * **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method).
+ * **Distance upstream from a peak to allow a pair** - The maximum distance (inclusive) upstream on the opposite strand from the primary peak to locate another peak, resulting in a pair.
+ * **Distance downstream from a peak to allow a pair** - The maximum distance (inclusive) downstream on the opposite strand from the primary peak to locate another peak, resulting in a pair.
+ * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold.
+ * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold.
+ * **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types.
+ 
+-----
+
 **Output Data Files**
 
  * **closest/largest/mode MP** - gff file containing the Matched Pairs and includes the peak-pair midpoint coordinate (column D) and the coordinate +1 (column E).  The tag count sum is reported in column F, along with the C-W distance in bp in column I.
@@ -169,17 +180,6 @@
  * **closest/largest/mode F** - pdf file that provides the final plots graph.
  * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs).
 
------
-
-**Options**
-
- * **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method).
- * **Distance upstream from a peak to allow a pair** - The maximum distance (inclusive) upstream on the opposite strand from the primary peak to locate another peak, resulting in a pair.
- * **Distance downstream from a peak to allow a pair** - The maximum distance (inclusive) downstream on the opposite strand from the primary peak to locate another peak, resulting in a pair.
- * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold.
- * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold.
- * **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types.
-
     </help>
     <expand macro="citations" />
 </tool>