--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_predictd.xml	Tue Jan 21 11:50:01 2014 -0500
@@ -0,0 +1,66 @@
+<tool id="macs2_predict" name="Predict" version="2.0.10.0">
+    <description>d or fragment size from alignment results</description>
+    <expand macro="requirements">
+        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
+    </expand>
+    <expand macro="version_command" />
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
+    <command>
+        macs2 predict
+            -i #echo ','.join($infiles)#
+            --tsize $tsize
+            @effective_genome_size@
+            --bw $band_width
+            --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi
+            &gt; $outfile;
+
+        Rscript predicted_model.R &gt; $outfile_image
+    </command>
+        <expand macro="stdio" />
+    <inputs>
+        <repeat name="infiles" title="ChIP-seq alignment files" min="1" 
+            help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command.">
+
+            <param name="infile" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-seq alignment file" help="-i" />
+        </repeat>
+
+        <expand macro="conditional_effective_genome_size" />
+        <expand macro="tag_size" />
+
+        <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
+            help="This value is only used while building the shifting model. (--bw)" />
+
+        <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
+            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
+        <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
+            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
+
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
+        <data name="outfile_image" format="png" label="${tool.name} on ${on_string} - X-correlation image" />
+    </outputs>
+    <tests>
+        <!--none yet for macs2-->
+    </tests>
+    <help>
+**What it does**
+
+bdgdiff from macs2
+
+
+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.
+    </help>
+</tool>