# HG changeset patch
# User iuc
# Date 1390480433 18000
# Node ID 8e2039b920bfa28beddf3135db2fe1a7af1dba02
# Parent 16dc0e3d659bb321392a1f80272dc333708ade53
Uploaded
diff -r 16dc0e3d659b -r 8e2039b920bf macs2_bdgbroadcall.xml
--- a/macs2_bdgbroadcall.xml Thu Jan 23 07:30:06 2014 -0500
+++ b/macs2_bdgbroadcall.xml Thu Jan 23 07:33:53 2014 -0500
@@ -37,12 +37,6 @@
Call broad peaks from bedGraph output.
bdgbroadcall from macs2
-------
-
-**Citation**
-
-For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
-
-Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
+@citation@
diff -r 16dc0e3d659b -r 8e2039b920bf macs2_bdgcmp.xml
--- a/macs2_bdgcmp.xml Thu Jan 23 07:30:06 2014 -0500
+++ b/macs2_bdgcmp.xml Thu Jan 23 07:33:53 2014 -0500
@@ -73,12 +73,6 @@
**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.
-------
-
-**Citation**
-
-For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
-
-Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
+@citation@
diff -r 16dc0e3d659b -r 8e2039b920bf macs2_bdgdiff.xml
--- a/macs2_bdgdiff.xml Thu Jan 23 07:30:06 2014 -0500
+++ b/macs2_bdgdiff.xml Thu Jan 23 07:33:53 2014 -0500
@@ -71,12 +71,6 @@
bdgdiff from macs2
-------
-
-**Citation**
-
-For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
-
-Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
+@citation@
diff -r 16dc0e3d659b -r 8e2039b920bf macs2_bdgpeakcall.xml
--- a/macs2_bdgpeakcall.xml Thu Jan 23 07:30:06 2014 -0500
+++ b/macs2_bdgpeakcall.xml Thu Jan 23 07:33:53 2014 -0500
@@ -43,12 +43,6 @@
bdgpeakcall from macs2
-------
-
-**Citation**
-
-For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
-
-Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
+@citation@
diff -r 16dc0e3d659b -r 8e2039b920bf macs2_callpeak.xml
--- a/macs2_callpeak.xml Thu Jan 23 07:30:06 2014 -0500
+++ b/macs2_callpeak.xml Thu Jan 23 07:33:53 2014 -0500
@@ -224,12 +224,6 @@
**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.
-------
-
-**Citation**
-
-For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
-
-Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
+@citation@
diff -r 16dc0e3d659b -r 8e2039b920bf macs2_filterdup.xml
--- a/macs2_filterdup.xml Thu Jan 23 07:30:06 2014 -0500
+++ b/macs2_filterdup.xml Thu Jan 23 07:33:53 2014 -0500
@@ -53,12 +53,7 @@
Remove duplicate reads at the same position, then convert acceptable format to BED format.
filterdup tool from macs2
-------
-**Citation**
-
-For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
-
-Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
+@citation@
diff -r 16dc0e3d659b -r 8e2039b920bf macs2_macros.xml
--- a/macs2_macros.xml Thu Jan 23 07:30:06 2014 -0500
+++ b/macs2_macros.xml Thu Jan 23 07:33:53 2014 -0500
@@ -44,4 +44,14 @@
+
+
+------
+
+**Citation**
+
+For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
+
+Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening.
+
diff -r 16dc0e3d659b -r 8e2039b920bf macs2_predict.xml
--- a/macs2_predict.xml Thu Jan 23 07:30:06 2014 -0500
+++ b/macs2_predict.xml Thu Jan 23 07:33:53 2014 -0500
@@ -55,12 +55,6 @@
Note that pair-end data is not supposed to work with this command.
-------
-
-**Citation**
-
-For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
-
-Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
+@citation@
diff -r 16dc0e3d659b -r 8e2039b920bf macs2_randsample.xml
--- a/macs2_randsample.xml Thu Jan 23 07:30:06 2014 -0500
+++ b/macs2_randsample.xml Thu Jan 23 07:33:53 2014 -0500
@@ -50,12 +50,7 @@
**What it does**
randsample tool from macs2
-------
-**Citation**
-
-For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
-
-Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
+@citation@
diff -r 16dc0e3d659b -r 8e2039b920bf macs2_refinepeak.xml
--- a/macs2_refinepeak.xml Thu Jan 23 07:30:06 2014 -0500
+++ b/macs2_refinepeak.xml Thu Jan 23 07:33:53 2014 -0500
@@ -33,12 +33,6 @@
(Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP.
-------
-
-**Citation**
-
-For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
-
-Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
+@citation@