<tool id="bs_seeker_wrapper" name="BS-Seeker2" version="2.0.0">
  <requirements><requirement type='package'>bs_seeker2</requirement></requirements>
  <description>Versatile aligner for bisulfite sequencing data</description>
  <command interpreter="python">
      bs_seeker2_wrapper.py
      ### define exec path
      ###    --exec-path "/u/home/galaxy/galaxy/GalaxyTools/bin"
      ### [Please change the following path to your local directory]
          --exec-path "/Users/weilong/Documents/program/BSseeker2"
      ### output
          --align--output $align_output
          --call_methylation--wig $call_methylation_wig
          --call_methylation--CGmap $call_methylation_CGmap
          --call_methylation--ATCGmap $call_methylation_ATCGmap
          --call_methylation--txt

      #if $singlePaired.sPaired == "paired"
          --align--input_1 $input1
          --align--input_2 $singlePaired.input2
      #end if


      ### aligner
      --align--aligner ${choosealigner.aligner}
      #if $choosealigner.aligner == "bowtie2"
          #if $choosealigner.mode_type == "local"
              --align--bt2--local
          #else
              --align--bt2--end-to-end
          #end if
      #end if

      ### Index from history or built-in
      #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history"
          --build--file ${choosealigner.rrbsFragments.refGenomeSource.ownFile}
          --build--aligner ${choosealigner.aligner}
          --align-g ${choosealigner.rrbsFragments.refGenomeSource.ownFile}
          --align--db ${choosealigner.rrbsFragments.refGenomeSource.ownFile}
      #else if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "indexed"
          --align--db ${choosealigner.rrbsFragments.refGenomeSource.index.fields.path}
          --align-g ${choosealigner.rrbsFragments.refGenomeSource.index.fields.path}/${choosealigner.rrbsFragments.refGenomeSource.index.fields.dbkey}.fa

      #end if

      ### RRBS or WGBS
      #if $choosealigner.rrbsFragments.Fragmented == "Yes"
          #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history"
            --build--rrbs
            --build--low ${choosealigner.rrbsFragments.lowerBound}
            --build--up ${choosealigner.rrbsFragments.upperBound}
          #end if
          --align--rrbs
          --align--low ${choosealigner.rrbsFragments.lowerBound}
          --align--up ${choosealigner.rrbsFragments.upperBound}
      #end if



      ### Inputs
      #if $singlePaired.sPaired == "single"
          --align-i $input1
      #end if

      ### Library type
          --align-t $tag

      ### other general options
      #if $sParams.sSettingsType == "preSet"
          --align--start_base 1
          --align--end_base 200
          --align--mis 4
      #end if

      ### adapter information
      #if $adapterInfo.useAdapter == "Yes"
          --align--adapter ${adapterInfo.adapter_file}
      #end if

      #if $sParams.sSettingsType == "full"
          --align--start_base ${sParams.start_base}
          --align--end_base ${sParams.end_base}
          --align--mis ${sParams.num_mismatch}
      #end if

  </command>
  <inputs>
     <param format="fastq,fasta,qseq" name="input1" type="data" label="Input your read file" help="reads file in fastq, qseq or fasta format" />
     <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="paired">
          <param format="fastq,fasta,qseq" name="input2" type="data" label="Input your read file 2" help="reads in fastq, qseq or fasta format" />
          <param name="min_ins_distance" type="integer" value="-1" label=" Minimum insert size for valid paired-end alignments" />
          <param name="max_ins_distance" type="integer" value="400" label="Maximum insert size for valid paired-end alignments" />
        </when>
     </conditional> 
     <param name="tag" type="select" label="Type of libraries">
        <option value="N">directional libraries</option>
        <option value="Y">undirectional libraries</option>
     </param>
     <conditional name="choosealigner">
         <param name="aligner" type="select" label="Short reads aligner">
             <option value="bowtie">bowtie</option>
             <option value="bowtie2">bowtie2</option>
         </param>
         <when value="bowtie">
             <conditional name="rrbsFragments">
                 <param name="Fragmented" type="select" label="RRBS-seq reads" help="">
                     <option value="No">No</option>
                     <option value="Yes">Yes</option>
                 </param>
                 <when value="Yes">
                     <param name="lowerBound" type="integer" value="40" label="The lower bound for RRBS fragments" help="Default: 40" />
                     <param name="upperBound" type="integer" value="500" label="The upper bound for RRBS fragments" help="Default: 500" />
                     <conditional name="refGenomeSource">
                         <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="">
                             <option value="indexed">Use a built-in index</option>
                             <option value="history">Use one from the history</option>
                         </param>
                         <when value="indexed">
                             <param name="index" type="select" label="Select a reference genome (RRBS, bowtie)">
                                 <options from_data_table="bs_seeker2_indexes_RRBS_bowtie">
                                     <filter type="sort_by" column="2"/>
                                     <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                                 </options>
                             </param>
                         </when>
                         <when value="history">
                             <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
                         </when>
                     </conditional>
                 </when>
                 <when value="No">
                     <conditional name="refGenomeSource">
                         <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="">
                             <option value="indexed">Use a built-in index</option>
                             <option value="history">Use one from the history</option>
                         </param>
                         <when value="indexed">
                             <param name="index" type="select" label="Select a reference genome (WGBS, bowtie)">
                                 <options from_data_table="bs_seeker2_indexes_WGBS_bowtie">
                                     <filter type="sort_by" column="2"/>
                                     <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                                 </options>
                             </param>
                         </when>
                         <when value="history">
                             <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
                         </when>
                     </conditional>
                 </when>
             </conditional>
         </when>

         <when value="bowtie2">
             <conditional name="rrbsFragments">
                 <param name="Fragmented" type="select" label="RRBS-seq reads" help="">
                     <option value="No">No</option>
                     <option value="Yes">Yes</option>
                 </param>
                 <when value="Yes">
                     <param name="lowerBound" type="integer" value="40" label="The lower bound for RRBS fragments" help="Default: 40" />
                     <param name="upperBound" type="integer" value="500" label="The upper bound for RRBS fragments" help="Default: 500" />
                     <conditional name="refGenomeSource">
                         <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="">
                             <option value="indexed">Use a built-in index</option>
                             <option value="history">Use one from the history</option>
                         </param>
                         <when value="indexed">
                             <param name="index" type="select" label="Select a reference genome (RRBS, bowtie2)">
                                 <options from_data_table="bs_seeker2_indexes_RRBS_bowtie2">
                                     <filter type="sort_by" column="2"/>
                                     <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                                 </options>
                             </param>
                         </when>
                         <when value="history">
                             <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
                         </when>
                     </conditional>
                 </when>
                 <when value="No">
                     <conditional name="refGenomeSource">
                         <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="">
                             <option value="indexed">Use a built-in index</option>
                             <option value="history">Use one from the history</option>
                         </param>
                         <when value="indexed">
                             <param name="index" type="select" label="Select a reference genome (WGBS, bowtie2)">
                                 <options from_data_table="bs_seeker2_indexes_WGBS_bowtie2">
                                     <filter type="sort_by" column="2"/>
                                     <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                                 </options>
                             </param>
                         </when>
                         <when value="history">
                             <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
                         </when>
                     </conditional>
                 </when>
             </conditional>


             <conditional name="mode_type">
                 <param name="mode" type="select" label="Select the mode of Bowtie2">
                     <option value="local" selected="true"> local alignment </option>
                     <option value="end_to_end" > end-to-end alignment </option>
                 </param>
             </conditional>
         </when>
     </conditional>
     <conditional name="adapterInfo">
        <param name="useAdapter" type="select" label="adapter sequence">
           <option value="noAdapter">No</option>
           <option value="withAdapter">Yes</option>
        </param>
        <when value="withAdapter">
           <param format="txt" name="adapter_file" type="data" label="Input file of your adaptor sequences" help="Input text file of your adaptor sequences" />
        </when>
     </conditional>

     <conditional name="sParams">
       <param name="sSettingsType" type="select" label="BS Seeker2 settings to use" help="You can use the default settings or set customer values for the BS Seeker2 parameters.">
         <option value="preSet">User Defaults</option>
         <option value="full">Full parameter list</option>
       </param>
       <when value="preSet" /> 
       <when value="full">
           <param name="start_base" type="integer" value="1" label="The start base of the read to be mapped" help="" />
           <param name="end_base" type="integer" value="200" label="The end base of the read to be mapped" help="" />

           <param name="num_mismatch" type="integer" value="4" label="Number of mismatches" help="(INT) Default: 4" />
       </when>   
     </conditional>

</inputs>

  <outputs>
    <data format="bam" name="align_output"  label="BAM Alignments"> </data>
    <data format="wig" name="call_methylation_wig"  label="Methylation Levels"> </data>
    <data format="tabular" name="call_methylation_CGmap"  label="CGmap file"> </data>
    <data format="tabular" name="call_methylation_ATCGmap"  label="ATCGmap file"> </data>

  </outputs>
  <help>
**What it does**

BS-Seeker2 is a seamlessly pipeline for mapping bisulfite sequencing data and generating detailed DNA methylome. BS-Seeker2 improves mappability by using local alignment, and is tailored for RRBS library by building special index, with higher efficiency and accuracy. This is the Galaxy version of BS-Seeker2.

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**Resources**

The homepage for BS-Seeker2 is http://pellegrini.mcdb.ucla.edu/BS_Seeker2/.

For more information of BS-Seeker2, please refer to https://github.com/BSSeeker/BSseeker2.

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**Example**

- Adapter file::

      AGATCGGAAGAGCACACGTC


  </help>
</tool>