--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_bdgcmp.xml	Wed Feb 11 10:18:02 2015 -0500
@@ -0,0 +1,81 @@
+<tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="@VERSION_STRING@.0">
+    <description>Deduct noise by comparing two signal tracks in bedGraph</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
+    <command>
+        macs2 bdgcmp
+            -t "${ infile_treatment }"
+            -c "${ infile_control }"
+
+            -m "${ bdgcmp_options.bdgcmp_options_selector }"
+            #if str($bdgcmp_options.bdgcmp_options_selector) in ['FE', 'logFE', 'logLR']:
+                -p "${ bdgcmp_options.pseudocount }"
+            #end if
+            -o "${ outfile }"
+
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile_treatment" type="data" format="bedgraph" label="Treatment bedGraph file" />
+        <param name="infile_control" type="data" format="bedgraph" label="Control bedGraph file" />
+
+        <conditional name="bdgcmp_options">
+            <param name="bdgcmp_options_selector" type="select" label="Method to use while calculating a score in any bin by comparing treatment value and control value">
+                <option value="ppois" selected="true">Poisson pvalue (-log10) using control as lambda and treatment as observation (ppois)</option>
+                <option value="qpois">q-value through a BH process for poisson pvalues (qpois)</option>
+                <option value="subtract">subtraction from treatment (subtract)</option>
+                <option value="logFE">log10 fold enrichment (logFE)</option>
+                <option value="FE">linear scale fold enrichment (FE)</option>
+                <option value="logLR">log10 likelihood between ChIP-enriched model and open chromatin model (logLR)</option>
+                <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models (slogLR)</option>
+            </param>
+            <when value="FE">
+                <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/>
+            </when>
+            <when value="logLR">
+                <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/>
+            </when>
+            <when value="logFE">
+                <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/>
+            </when>
+            <when value="ppois"/>
+            <when value="qpois"/>
+            <when value="subtract"/>
+            <when value="slogLR"/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="bedgraph" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile_control" value="callpeak_control_part.bdg" ftype="bedgraph"/>
+            <param name="infile_treatment" value="callpeak_treatment_part.bdg" ftype="bedgraph"/>
+            <param name="bdgcmp_options_selector" value="slogLR"/>
+            <output name="outfile" file="bdgcmp_on_Control_and_ChIP_slogLR.bdg"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq)
+is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for
+identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of
+binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
+
+View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README
+
+------
+
+**Usage**
+
+**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.
+
+
+@citation@
+    </help>
+    <expand macro="citations" />
+</tool>