<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>