--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/methylation_analysis_bismark/methylation_analysis/differential_methylation.xml	Tue Dec 04 20:15:26 2012 -0500
@@ -0,0 +1,113 @@
+<tool id="differential_methylation_tool" name="Differential Methylation" version="1.0.0">
+  <description>methylation status of two samples by region</description>
+  <requirements>
+    <requirement type="package" version="0.1.16">samtools</requirement>
+    <requirement type="package" version="0.12.7">bowtie2</requirement>
+    <requirement type="package" >getopt</requirement>
+    <requirement type="package" >snow</requirement>
+    <requirement type="package" >abind</requirement>
+    <requirement type="package" >rtracklayer</requirement>
+    <requirement type="package" >biomaRt</requirement>
+
+  </requirements>
+  <command >
+    
+	differential_methylation.R -s $seg1 -t $seg2 -r $genome.fields.dbkey -p 1 -f $fdr -a $annot -o $output 2>1
+
+  </command>
+	<inputs>
+	
+		<param name="seg1" type="data" format="tabular" label="Seg file 1" />
+		<param name="seg2" type="data" format="tabular" label="Seg file 2" />
+		
+		<param name="genome" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+			<options from_data_table="bismark_indexes">
+				<filter type="sort_by" column="2"/>
+				<validator type="no_options" message="No indexes are available for the selected input dataset"/>
+			</options>
+		</param>
+		<param name="annot" type="select" label="Annotation">
+			<option value="both" selected="true">both</option>
+			<option value="gene">gene</option>
+			<option value="cpg">cpg</option>
+		</param>
+		<param name="fdr" type="select" label="fdr method">
+			<option value="none" selected="true">none</option>
+			<option value="holm">holm</option>
+			<option value="hochberg">hochberg</option>
+			<option value="hommel">hommel</option>
+			<option value="bonferroni">bonferroni</option>
+			<option value="BH">BH</option>
+			<option value="BY">BY</option>
+			<option value="fdr">fdr</option>															
+		</param>
+		
+		
+			
+	</inputs>
+	<outputs>
+		<data format="tabular" name="output" label="${tool.name} on ${on_string}">
+			<actions>
+				<action type="metadata" name="dbkey">
+					<option type="from_data_table" name="bismark_indexes" column="1" offset="0">
+					<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+					<filter type="param_value" ref="genome" column="0"/>
+					</option>
+				</action>
+			</actions>
+		</data>
+		
+	</outputs>
+	<help>
+|
+
+**What it does**
+
+Compares the methylation status of two samples by region. It calculates a p.value for differential methylation using a test of proportions, that is, it tests the null hypothesis that the 2 methylation proportions are equal. The script will also calculate the difference in methylation and annotate the regions with the closest ensembl gene and cpg island. This script takes as input two seg files created by the tool "methylation_by_region_converter" and returns a new seg file containing:
+
+::
+
+  Comparison the name of the comparison
+  Chrom the chromosome of the region
+  loc.start the start of the region
+  loc.end the end of the region
+  Sample1.Methylated the number of methylated reads in the region for sample 1
+  Sample1.Total the total number of reads in the region for sample 1
+  Sample1.Proportion the proportion of methylated reads for sample 1
+  Sample2.Methylated the number of methylated reads in the region for sample 2
+  Sample2.Total the total number of reads in the region for sample 2
+  Sample2.Proportion the proportion of methylated reads for sample 2
+  X_Squared the test statistic for the test of proportions
+  P.value the raw p-value
+  P.adjusted the fdr adjusted p-value
+  ensembl_gene_id the closest or overlapping Ensembl gene id
+  hgnc_symbol the HUGO Gene Nomenclature Committee id
+  refseq_mrna the refseq id
+  feature_start the start of the gene
+  feature_end the end of the gene
+  Distance_To_Feature the distance to the feature
+  Cpg the closest or overlapping CpG island
+  cpg_perCpg the number of CpGs in island
+  cpg_perGc the percentage of island that is CpG
+  cpg_start the start location of the CpG island
+  cpg_end the end location of the CpG island
+  Distance_To_cpg the distance to the CpG island
+  DiffProp the difference in the methylation proportions
+
+  Usage: differential_methylation.R [[option][value]]
+  Options:
+  -h|--help         view this help
+  -s|--segfile1     seg file 1
+  -t|--segfile2     seg file 2
+  -o|--output       output file
+  -f|--fdr          fdr method [holm|hochberg|hommel|bonferroni|BH|BY|fdr|none]
+  -r|--reference    reference to use [hg19|GRCh37|mm9|NCBIM37|mm10|GRCm38|dm3|BDGP5]
+  -a|--annot        annotation to add [both|gene|cpg]
+  -p|--processes    number of cluster instances to open [1]
+
+
+
+	</help>
+</tool>
+
+