--- a/macs2_macros.xml	Mon Feb 06 02:30:37 2017 -0500
+++ b/macs2_macros.xml	Sat Apr 08 08:28:57 2017 -0400
@@ -1,31 +1,30 @@
 <macros>
+    <token name="@VERSION_STRING@">2.1.1.20160309</token>
+
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.1.0.20151222">macs2</requirement>
-            <requirement type="package" version="1.7.1">numpy</requirement>
-            <requirement type="package" version="0.12.0">scipy</requirement>
+            <requirement type="package" version="@VERSION_STRING@">macs2</requirement>
             <yield />
         </requirements>
     </xml>
 
-    <token name="@VERSION_STRING@">2.1.0.20151222</token>
-
     <xml name="conditional_effective_genome_size">
         <conditional name="effective_genome_size_options">
             <param name="effective_genome_size_options_selector" type="select" label="Effective genome size"
-                help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
-                    Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
-                    See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes. (--gsize)">
-                <option value="2451960000">Human (2,451,960,000)</option>
-                <option value="2150570000">Mouse (2,150,570,000)</option>
-                <option value="121400000">Fly (121,400,000)</option>
-                <option value="93260000">Worm (93,260,000)</option>
+                help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of Ns that should be discarded.
+                Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. (--gsize)">
+                <option value="2451960000">H. sapiens (2,451,960,000)</option>
+                <option value="2150570000">M. musculus (2,150,570,000)</option>
+                <option value="121400000">D. melanogaster (121,400,000)</option>
+                <option value="93260000">C. elegans (93,260,000)</option>
+                <option value="12400000">S. cerevisiae (12,400,000)</option>
                 <option value="user_defined">User defined</option>
             </param>
             <when value="2451960000" />
             <when value="2150570000" />
             <when value="121400000" />
             <when value="93260000" />
+            <when value="12400000" />
             <when value="user_defined">
                 <param name="gsize" type="integer" label="Effective genome size" value=""/>
             </when>
@@ -51,11 +50,22 @@
         </conditional>
     </xml>
 
+    <xml name="mfold_options">
+        <section name="mfold" title="Mfold settings" expanded="True" help="Select the regions within MFOLD range of highconfidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than upper limit, and higher than the lower limit. Default is 5 for lower and 50 for upper (--mfold)" >
+            <param name="lower" type="integer" value="5" label="Set lower mfold bound" />
+            <param name="upper" type="integer" value="50" label="Set upper mfold bound" />
+        </section>
+    </xml>
+
+    <token name="@mfold_command@">
+        --mfold '${mfold.lower}' '${mfold.upper}'
+    </token>
+
     <token name="@effective_genome_size@">
-        #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined':
-            --gsize "${ effective_genome_size_options.gsize }"
+        #if $effective_genome_size_options.effective_genome_size_options_selector == "user_defined":
+            --gsize '${ effective_genome_size_options.gsize }'
         #else:
-            --gsize "${ effective_genome_size_options.effective_genome_size_options_selector }"
+            --gsize '${ effective_genome_size_options.effective_genome_size_options_selector }'
         #end if
     </token>
 
@@ -64,16 +74,18 @@
     </xml>
 
     <xml name="tag_size">
-        <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will override the auto detected tag size. Per default that option is deactivated: -1.0 (--tsize)" />
+        <param name="tsize" type="integer" label="Tag size" value="" optional="true"
+               help="This will override the auto detected tag size. Per default that option is deactivated: -1.0 (--tsize)" />
     </xml>
     <xml name="band_width">
-        <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
-            help="This value is only used while building the shifting model. (--bw)" />
+        <param name="band_width" type="integer" value="300"
+               label="Band width for picking regions to compute fragment size"
+               help=" You can set this parameter as the medium fragment size expected from sonication or size selection. (--bw)" />
     </xml>
 
     <token name="@tag_size@">
-        #if $tsize == -1.0:
-            --tsize "${ tsize }"
+        #if $tsize:
+            --tsize '${ tsize }'
         #end if
     </token>
 
@@ -89,15 +101,13 @@
     <token name="@citation@">
 ------
 
-**Citation**
+Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening.
 
-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>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1186/gb-2008-9-9-r137</citation>
+            <citation type="doi">10.1038/nprot.2012.101</citation>
         </citations>
     </xml>
 </macros>