<tool id="bismark_methylation_extractor" name="Bismark" version="0.7.12">
    <!-- Wrapper compatible with Bismark version 0.7.7 -->
    <description>methylation extractor</description>
    <!--<version_command>bismark_methylation_extractor version</version_command>-->
    <requirements>
        <requirement type="set_environment">SCRIPT_PATH</requirement>
        <requirement type="package" version="0.12.8">bowtie</requirement>
        <requirement type="package" version="2.0.0-beta7">bowtie2</requirement>
    </requirements>
    <parallelism method="basic"></parallelism>
    <command interpreter="python">
        bismark_methylation_extractor.py

        --infile $input

        --bismark_path \$SCRIPT_PATH

        #if $singlePaired.sPaired == "single":
            --single-end
        #else:
            --paired-end
            $singlePaired.no_overlap
        #end if

        #if str($ignore_bps) != "0":
           --ignore $ignore_bps
        #end if

        #if $report:
            --report-file $o_report
        #end if

        #if $comprehensive:
            --comprehensive
        #end if

        #if $merge_non_cpg:
            --merge-non-cpg
        #end if

        #if $compress:
            --compress $compressed_output
        #else:
            #if $comprehensive == False and $merge_non_cpg == False:
                ##twelfe files
                --cpg_ot $cpg_ot
                --chg_ot $chg_ot
                --chh_ot $chh_ot
                --cpg_ctot $cpg_ctot
                --chg_ctot $chg_ctot
                --chh_ctot $chh_ctot
                --cpg_ob $cpg_ob
                --chg_ob $chg_ob
                --chh_ob $chh_ob
                --cpg_ctob $cpg_ctob
                --chg_ctob $chg_ctob
                --chh_ctob $chh_ctob
            #elif $merge_non_cpg and $comprehensive:
                ## two files
                --non_cpg_context $non_cpg_context
                --cpg_context $cpg_context
            #elif $comprehensive:
                ## three files
                --cpg_context $cpg_context
                --chg_context $chg_context
                --chh_context $chh_context
            #elif $merge_non_cpg:
                ## eight files
                --non_cpg_context_ctot $non_cpg_context_ctot
                --non_cpg_context_ot $non_cpg_context_ot
                --non_cpg_context_ob $non_cpg_context_ob
                --non_cpg_context_ctob $non_cpg_context_ctob
                --cpg_ot $cpg_ot
                --cpg_ctot $cpg_ctot
                --cpg_ob $cpg_ob
                --cpg_ctob $cpg_ctob
            #end if
        ## end compress
        #end if

    </command>
    <inputs>
        <!-- Input Parameters -->
        <param name="input" type="data" format="sam" label="SAM file from Bismark bisulfid mapper" />
        <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" />
            <when value="paired">
                <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="This option avoids scoring overlapping methylation calls twice, in case of overlapping read one and read two" help="" />
            </when>
        </conditional>

       <param name="ignore_bps" type="integer" value="0" label="Ignore the first N bp when processing the methylation call string" />
       <param name="comprehensive" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all four possible strand-specific methylation info
into context-dependent output files" help="" />
       <param name="merge_non_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all non-CpG contexts into one file" help="This will produce eight strand-specific output files, or two output files in comprehensive mode." />
       <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Short methylation summary output" />
       <param name="compress" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Compress all result files and output one single file" />

    </inputs>
    <outputs>
        <!--
            OT – original top strand
            CTOT – complementary to original top strand
            OB – original bottom strand
            CTOB – complementary to original bottom strand
        -->
        <data format="tabular" name="o_report" label="${tool.name} on ${on_string}: Report file">
          <filter> ( report is True ) </filter>
        </data>

        <!-- default output 12 files -->
        <data format="tabular" name="cpg_ot" label="${tool.name} on ${on_string}: CpG original top strand">
          <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
        </data>
        <data format="tabular" name="chg_ot" label="${tool.name} on ${on_string}: CHG original top strand">
          <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
        </data>
        <data format="tabular" name="chh_ot" label="${tool.name} on ${on_string}: CHH original top strand">
          <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
        </data>
        <data format="tabular" name="cpg_ctot" label="${tool.name} on ${on_string}: CpG complementary to top strand">
          <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
        </data>
        <data format="tabular" name="chg_ctot" label="${tool.name} on ${on_string}: CHG complementary to top strand">
          <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
        </data>
        <data format="tabular" name="chh_ctot" label="${tool.name} on ${on_string}: CHH complementary to top strand">
          <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
        </data>

        <data format="tabular" name="cpg_ob" label="${tool.name} on ${on_string}: CpG original bottom strand">
          <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
        </data>
        <data format="tabular" name="chg_ob" label="${tool.name} on ${on_string}: CHG original bottom strand">
          <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
        </data>
        <data format="tabular" name="chh_ob" label="${tool.name} on ${on_string}: CHH original bottom strand">
          <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
        </data>
        <data format="tabular" name="cpg_ctob" label="${tool.name} on ${on_string}: CpG complementary to bottom strand">
          <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
        </data>
        <data format="tabular" name="chg_ctob" label="${tool.name} on ${on_string}: CHG complementary to bottom strand">
          <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
        </data>
        <data format="tabular" name="chh_ctob" label="${tool.name} on ${on_string}: CHH complementary to bottom strand">
          <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
        </data>

        <!-- Context-dependent methylation output files (comprehensive option) -->
        <data format="tabular" name="cpg_context" label="${tool.name} on ${on_string}: CpG context dependent">
          <filter> ( compress == False and comprehensive) </filter>
        </data>
        <data format="tabular" name="chg_context" label="${tool.name} on ${on_string}: CHG context dependent">
          <filter> ( compress == False and comprehensive and merge_non_CpG == False) </filter>
        </data>
        <data format="tabular" name="chh_context" label="${tool.name} on ${on_string}: CHH context dependent">
          <filter> ( compress == False and comprehensive and merge_non_CpG == False) </filter>
        </data>

        <data format="tabular" name="non_cpg_context" label="${tool.name} on ${on_string}: Non CpG context dependent">
          <filter> ( compress == False and comprehensive and merge_non_cpg) </filter>
        </data>

        <data format="tabular" name="non_cpg_context_ot" label="${tool.name} on ${on_string}: Non CpG context dependent on original top strand">
          <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter>
        </data>
        <data format="tabular" name="non_cpg_context_ctot" label="${tool.name} on ${on_string}: Non CpG context dependent on complementary to top strand">
          <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter>
        </data>
        <data format="tabular" name="non_cpg_context_ob" label="${tool.name} on ${on_string}: Non CpG context dependent on bottom top strand">
          <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter>
        </data>
        <data format="tabular" name="non_cpg_context_ctob" label="${tool.name} on ${on_string}: Non CpG context dependent on complementary to bottom strand">
          <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter>
        </data>

        <data format="gzipped" name="compressed_output" label="${tool.name} on ${on_string}: Result archive.">
          <filter> ( compress ) </filter>
        </data>
    </outputs>

    <tests>
    </tests>

    <help>

**What it does**

The following is a brief description of all options to control the Bismark_
methylation extractor. The script reads in a bisulfite read alignment results file 
produced by the Bismark bisulfite mapper and extracts the methylation information
for 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


The methylation extractor outputs result files for cytosines in CpG, CHG and CHH
context (this distinction is actually already made in Bismark itself). As the methylation
information for every C analysed can produce files which easily have tens or even hundreds of
millions of lines, file sizes can become very large and more difficult to handle. The C
methylation info additionally splits cytosine methylation calls up into one of the four possible
strands a given bisulfite read aligned against:

  - OT = original top strand
  - CTOT = complementary to original top strand

  - OB = original bottom strand
  - CTOB = complementary to original bottom strand

Thus, by default twelve individual output files are being generated per input file (unless
--comprehensive is specified, see below). The output files can be imported into a genome
viewer, such as SeqMonk, and re-combined into a single data group if desired (in fact
unless the bisulfite reads were generated preserving directionality it doesn't make any
sense to look at the data in a strand-specific manner). Strand-specific output files can
optionally be skipped, in which case only three output files for CpG, CHG or CHH context
will be generated. For both the strand-specific and comprehensive outputs there is also
the option to merge both non-CpG contexts (CHG and CHH) into one single non-CpG context.


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


It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2.

-------

**Bismark settings**

All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin.

------

**Outputs**

The output files are in the following format (tab delimited)::


    Column  Description
  --------  --------------------------------------------------------
      1     seq-ID
      2     strand
      3     chromosome
      4     position
      5     methylation call


  * Methylated cytosines receive a '+' orientation,
  * Unmethylated cytosines receive a '-' orientation.

------

**OPTIONS**

Input::

  -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. Whilst this removes a bias towards more methylation calls
                           towards the center of sequenced fragments it can de facto remove
                           a good proportion of the data.

  --ignore INT             Ignore the first INT bp at the 5' end of each read when processing the
                           methylation call string. This can remove e.g. a restriction enzyme site
                           at the start of each read.

Output::

  --comprehensive          Specifying this option will merge all four possible strand-specific 
                           methylation info into context-dependent output files. The default 
                           contexts are:
                            - CpG context
                            - CHG context
                            - CHH context

  --merge_non_CpG          This will produce two output files (in --comprehensive mode) or eight
                           strand-specific output files (default) for Cs in
                            - CpG context
                            - non-CpG context

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


  </help>
</tool>