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changeset 9:8e2039b920bf draft

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Uploaded
author iuc
date Thu, 23 Jan 2014 07:33:53 -0500
parents 16dc0e3d659b
children 6f4e56ea7568
files macs2_bdgbroadcall.xml macs2_bdgcmp.xml macs2_bdgdiff.xml macs2_bdgpeakcall.xml macs2_callpeak.xml macs2_filterdup.xml macs2_macros.xml macs2_predict.xml macs2_randsample.xml macs2_refinepeak.xml
diffstat 10 files changed, 19 insertions(+), 61 deletions(-) [+]
line wrap: on
line diff
--- 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@
     </help>
 </tool>
--- 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@
     </help>
 </tool>
--- 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@
     </help>
 </tool>
--- 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@
     </help>
 </tool>
--- 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@
   </help>
 </tool>
--- 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@
   </help>
 </tool>
--- 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 @@
             <regex match="EXception:" />
         </stdio>
     </xml>
+
+    <token name="@citation@">
+------
+
+**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.
+    </token>
 </macros>
--- 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@
     </help>
 </tool>
--- 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@
   </help>
 </tool>
--- 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@
     </help>
 </tool>