<tool id="methyation_extractor_tool" name="Methylation Extractor" version="0.7.6">
  <description>: extracts the methylation information for individual cytosine</description>
  <requirements>
    <requirement type="package" version="0.1.16">samtools</requirement>
    <requirement type="package" version="0.12.7">bowtie2</requirement>
    <requirement type="package" version="0.7.6">bismark</requirement>
  </requirements>
  <command interpreter="perl">
    
	methylation_extractor_wrapper.pl
	
	
	"GENOME::${genome.fields.path}"      
	
	
	#if str($no_overlap) == "ON":
		"OPTION::--no_overlap"
	#end if
	
	#if str($ending) == "single":
		"ENDING::-s"
	#else
		"ENDING::-p"
	#end if
	
	#if str($report) == "ON":
		"OPTION::--report"
	#end if
	
	"OPTION::--bedGraph"
	
	"OPTION::--counts"
	
	
	"OUTPUT::$output"
	"SUMMARY::$summary"

	"BAMFILE::$bamfile"


  </command>
	<inputs>

		<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="bamfile" type="data" format="bam" label="Bam file: bismark output" />
		
		<param name="ending" type="select" label="ending" help="" optional="true">
			<option value="single" >single-end</option>
			<option value="paired" selected="true">paired-end</option>
		</param>
	
		<param name="no_overlap" type="select" label="no-overlap" help="" optional="true">
			<option value="ON" selected="true">ON</option>
			<option value="OFF">OFF</option>
		</param>
	
		<param name="report" type="select" label="Report" help="" optional="true">
			<option value="ON" selected="true">ON</option>
			<option value="OFF">OFF</option>
		</param>
	
	</inputs>
	<outputs>
		<data format="bedgraph" name="output" label="${tool.name} on ${on_string}">
			<actions>
				<action type="metadata" name="dbkey">
					<option type="from_data_table" name="bismark_indexes" column="1" offset="0">
					<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
					<filter type="param_value" ref="genome" column="0"/>
					</option>
				</action>
			</actions>
		</data>
		<data name="summary" format="txt" label="${tool.name} summary" />
	</outputs>
	<help>
|

**Reference**
	
  http://www.bioinformatics.babraham.ac.uk/projects/bismark/
  
-----

**What it does**



The script reads in a bisulfite read alignment results file 
produced by the Bismark bisulfite mapper (BAM file) and extracts the methylation 
informationfor individual cytosines. This information is found in the methylation 
call field which can contain the following characters:

::
       
 ~~~   X   for methylated C in CHG context (was protected)     ~~~
 
 ~~~   x   for not methylated C CHG (was converted)            ~~~
 
 ~~~   H   for methylated C in CHH context (was protected)     ~~~
 
 ~~~   h   for not methylated C in CHH context (was converted) ~~~
 
 ~~~   Z   for methylated C in CpG context (was protected)     ~~~
 
 ~~~   z   for not methylated C in CpG context (was converted) ~~~
 
 ~~~   .   for any bases not involving cytosines               ~~~
       


-----
 
**Required Parameters**

::

  -s/--single-end        Input file(s) are Bismark result file(s) generated from single-end
                         read data. Specifying either --single-end or --paired-end is
                         mandatory.

  -p/--paired-end        Input file(s) are Bismark result file(s) generated from paired-end
                         read data. Specifying either --paired-end or --single-end is
                         mandatory.

  --no_overlap           For paired-end reads it is theoretically possible that read_1 and
                         read_2 overlap. This option avoids scoring overlapping methylation
                         calls twice (only methylation calls of read 1 are used for in the process
                         since read 1 has historically higher quality basecalls than read 2).
                         Whilst this option removes a bias towards more methylation calls
                         in the center of sequenced fragments it may de facto remove a sizable
                         proportion of the data. This option is highly recommended for paired-end
                         data.

  --report               Prints out a short methylation summary as well as the paramaters used to run
                         this script.


-----

**Default Parameters**

::

  --bedGraph             After finishing the methylation extraction, the methylation output is written into a
                         sorted bedGraph file that reports the position of a given cytosine and its methylation 
                         state (in %, seem details below). The methylation extractor output is temporarily split up into
                         temporary files, one per chromosome (written into the current directory or folder
                         specified with -o/--output); these temp files are then used for sorting and deleted
                         afterwards. By default, only cytosines in CpG context will be sorted. The option
                         '--CX_context' may be used to report all cyosines irrespective of sequence context
                         (this will take MUCH longer!).



	</help>
</tool>