view bismark.xml @ 17:59a61c1d5aee draft default tip

Uploaded

<tool id="Bismark" name="Bismark Mapper">
        <requirements>
	    <requirement type='package'>
		Bismark
	    </requirement>
	</requirements>
	<command interpreter="bash">
               bismark_wrapper.sh
			##Reference genome
			ref="${indices.fields.path}"
			##Output files (SAM output, Bismark summary)
			mapped=$mapped
			summary=$summary
			##Temp directory
			tempdir=$mapped.files_path
			#if str($singlePaired.sPaired) == "single":
			  library=single
			  mate1=$singlePaired.sInput1
			  #if $singlePaired.sParams.sSettingsType == "full":
			    fullparam=true
			    qual=$singlePaired.sParams.qual
			    seedmms=$singlePaired.sParams.seedmms
			    seedlen=$singlePaired.sParams.seedlen
			    maqerr=$singlePaired.sParams.maqerr
			    directional=$singlePaired.sParams.non_directional
			    header=$singlePaired.sParams.sam_no_hd
			  #end if
			#else:
			  library=paired
			  mate1=$singlePaired.pInput1
			  mate2=$singlePaired.pInput2
			  #if $singlePaired.pParams.pSettingsType == "full":
			    fullparam="true"
			    qual=$singlePaired.pParams.qual
			    seedmms=$singlePaired.pParams.seedmms
			    seedlen=$singlePaired.pParams.seedlen
			    maqerr=$singlePaired.pParams.maqerr
			    directional=$singlePaired.pParams.non_directional
			    header=$singlePaired.pParams.sam_no_hd
			    minins=$singlePaired.pParams.minins
			    maxins=$singlePaired.pParams.maxins
			  #end if
			#end if
			
			
        </command>
  <inputs>
  <param name="indices" type="select" label="Select a reference genome">
	        	<options from_data_table="bismark_bs_indeces">
		        	<filter type="sort_by" column="2" />
	                	<validator type="no_options" message="No indexes are available" />
          		</options>
  </param>
  
  <conditional name="singlePaired">
      <param name="sPaired" type="select" label="Is this library mate-paired?">
        <option value="single">Single-end</option>
        <option value="paired">Paired-end</option>
      </param>
      <when value="single">
        <param name="sInput1" type="data" format="fastq" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
        <conditional name="sParams">
          <param name="sSettingsType" type="select" label="Bismark settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
            <option value="preSet">Commonly used</option>
            <option value="full">Full parameter list</option>
            </param>
          <when value="preSet" />
          <when value="full">
	    <param name="qual" type="select" label="Select the type of FastQ qualities">
		<option value="--phred33-quals">phred33-quals</option>
		<option value="--phred64-quals">phred64-quals</option>
		<option value="--solexa-quals">solexa-quals</option>
	    </param>
	    <param name="seedmms" type="integer" value="2" label="The maximum number of mismatches permitted in the seed" />
	    <param name="seedlen" type="integer" value="28" label="The seed length" />
	    <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the seed" />
	    <param name="non_directional" type="select" label="Is the library a non-directional one?">
	      <option value="">No</option>
	      <option value="--non_directional">Yes</option>
	    </param>
	    <param name="sam_no_hd" type="select" label="Should the SAM header lines (starting with @) be supressed?">
	      <option value="">No</option>
	      <option value="--sam-no-hd">Yes</option>
	    </param>
          </when> <!-- full -->
        </conditional> <!-- sParams -->
      </when> <!-- single -->
   
      <when value="paired">
        <param name="pInput1" type="data" format="fastq" label="Forward FASTQ file" />
	<param name="pInput2" type="data" format="fastq" label="Reverse FASTQ file" />

        <conditional name="pParams">
          <param name="pSettingsType" type="select" label="Bismark settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
            <option value="preSet">Commonly used</option>
            <option value="full">Full parameter list</option>
          </param>
          <when value="preSet" />
          <when value="full">
	    <param name="minins" type="integer" value="0" label="The minimum insert size for valid paired-end alignments" />
	    <param name="maxins" type="integer" value="500" label="The maximum insert size for valid paired-end alignments" />
	    <param name="qual" type="select" label="Select the type of FastQ qualities">
		<option value="--phred33-quals">phred33-quals</option>
		<option value="--phred64-quals">phred64-quals</option>
		<option value="--solexa-quals">solexa-quals</option>
	    </param>
	    <param name="seedmms" type="integer" value="2" label="The maximum number of mismatches permitted in the seed" />
	    <param name="seedlen" type="integer" value="28" label="The seed length" />
	    <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the seed" />
	    <param name="non_directional" type="select" label="Is the library a non-directional one?">
	      <option value="">No</option>
	      <option value="--non_directional">Yes</option>
	    </param>
	    <param name="sam_no_hd" type="select" label="Should the SAM header lines (starting with @) be supressed?">
	      <option value="">No</option>
	      <option value="--sam-no-hd">Yes</option>
	    </param>          
          </when> <!-- full -->
        </conditional> <!-- pParams -->
      </when> <!-- paired -->
    </conditional> <!-- singlePaired -->
  
  
 </inputs>
 <outputs>
        <data name="mapped" format="sam" label="Bismark Mapped Reads" />
	<data name="summary" format ="txt" label="Bismark Mapping Summary" />
 </outputs>
 <help>
**What it does**

Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. It's main features are:

   - Bisulfite mapping and methylation calling in one single step
   
   - Supports single-end and paired-end read alignments
   
   - Supports ungapped and gapped alignments
   
   - Alignment seed length, number of mismatches etc. are adjustable
   
   - Output discriminates between cytosine methylation in CpG, CHG and CHH context

.. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/

**Input formats**

Bismark accepts files in Sanger FASTQ format.

**Outputs**

The output is in SAM format, and has the following columns::

    Column  	Description
  --------  	--------------------------------------------------------   
  1 QNAME	seq-ID
  2 FLAG 	this flag tries to take the strand a bisulfite read originated from into account (this is different from ordinary DNA alignment flags!)
  3 RNAME 	chromosome
  4 POS 	start position
  5 MAPQ 	always 255
  6 CIGAR
  7 RNEXT
  8 PNEXT
  9 TLEN
 10 SEQ
 11 QUAL 	Phred33 scale
 12 NM-tag 	edit distance to the reference
 13 XX-tag 	base-by-base mismatches to the reference, not including indels
 14 XM-tag 	methylation call string
 15 XR-tag 	read conversion state for the alignment
 16 XG-tag 	genome conversion state for the alignment
   
 </help>
</tool>