[dspchip] r230 committed - Edited wiki page Usage through web user interface.

[dsp...@googlecode.com]

Revision: 230
Author: daweonline
Date: Fri Feb 11 02:34:30 2011
Log: Edited wiki page Usage through web user interface.
http://code.google.com/p/dspchip/source/detail?r=230

Modified:
/wiki/Usage.wiki

=======================================
--- /wiki/Usage.wiki Thu Feb 10 12:52:46 2011
+++ /wiki/Usage.wiki Fri Feb 11 02:34:30 2011
@@ -2,23 +2,23 @@

= `dspchip` command line options =

-`dspchip` comes with a number of options to perform signal analysis of a
ChIP-seq experiments.
+`dspchip` comes with a number of options to perform signal analysis of a
ChIP-seq experiments. These values apply to dspchip 0.7.7+

|| *Option* || *Type* || *Description* || *Accepted Values* || *Default
value* ||
-|| -i || Filename || Specify the ChIP file || Valid file || None ||
-|| -c || Filename || Specify the control file, can be either input or
another ChIP || Valid file || None ||
-|| --fa || String || File format for File A || sam bed wig bar bw || sam ||
-|| --fb || String || File format for File B || sam bed wig bar bw || None |
|
+|| -i, --sigA || Filename || Specify the ChIP file || Valid file || None |
|
+|| -c, --sigB || Filename || Specify the control file, can be either input
or another ChIP || Valid file || None ||
+|| --formatA || String || File format for File A || sam bed wig bar bw ||
sam ||
+|| --formatB || String || File format for File B || sam bed wig bar bw ||
None ||
|| -n, --name || String || Specify the experiment name || Escaped string |
| default ||
|| --pl || String || The signal analysis pipeline string || F W G A E N L
S R B Z || WES ||
-|| --wf || String || The windowing function when writing bedgraph || mean
med max || mean ||
+|| --winfun || String || The windowing function when writing bedgraph ||
mean med max || mean ||
|| --pf || String || Profile file format || bw bdg || bw ||
-|| -w, --wavelet || String || The wavelet to use. || Wavelet defined in
pywt or filter bank in INI file || coif4 ||
+|| -W, --wavelet || String || The wavelet to use. || Wavelet defined in
pywt or filter bank in INI file || coif4 ||
|| -C, --corr || Boolean || Perform correlation analysis || || False ||
|| -l, --baseline || String || Baseline function || min mad no || no ||
|| -e, --ewin || Float || Expected size for signal peaks in base pairs|| |
| 100000 ||
-|| --wstep || Float || Step size for windowing functions || || exp. size /
(1 + peak interspersion) ||
-|| -s, --bdgstep || Float || Step size for bedGraph output || || 10 ||
+|| -w, --wstep || Float || Step size for windowing functions || || exp.
size / (1 + peak interspersion) ||
+|| -s, --profstep || Float || Step size for profile output file || || 100 |
|
|| -r, --ratio || Float || Ratio of the max. peak heigth to split peaks ||
|| 0.3 ||
|| --ichrom || String || Include these chromosomes (comma separated) || ||
None ||
|| --echrom || String || Exclude these chromosomes (comma separated) || ||
None ||
@@ -29,9 +29,12 @@
|| --dist || String || Distribution model for peak p-value || hist wald ||
hist ||
|| -K || Float || Peak interspersion factor || || 0.5 ||
|| -q, --quality || Float || Min. mapping quality (for BAM files only) ||
|| 0.5 ||
+|| --downA || Float || Downsample ratio for signal A (only for intervals)
|| || 1.0 ||
+|| --downB || Float || Downsample ratio for signal B (only for
intervals) || || 1.0 ||
+|| --nodup || Boolean || Naive duplicate removal (only for sorted
intervals) || || False ||
|| --nosig || Boolean || Don't perform signal analysis (when you want to
call peaks from a wig) || || False ||
|| --nobdg || Boolean || Don't save a bedGraph file || || False ||
-|| --save || Boolean || Save chromosome data into numpy files (for
debugging issues) || || False ||
+|| --save || Boolean || Save chromosome data into numpy files (for
debugging purposes) || || False ||
|| --hist || Boolean || Save histograms for processed signals || || False |
|
|| --stats || Boolean || Save basic statistics || || False ||