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<tool id="bsfcall" name="bsfcall" version="1.0.0">
  <description>Mapping bisulfite-seq reads and calling methylated cytosines</description>
<!--
  <version_command></version_command>
-->

  <requirements>
    <requirement type="set_environment">TOOLDIR</requirement>
  </requirements>

  <command interpreter="perl">
    bsfcall_wrapper.pl TOOLDIR $reference.source $read.end \${GALAXY_SLOTS:-1} 

    #if $reference.source=="indexed":
      $reference.index.fields.path
    #else if $reference.source=="history":
      $reference.own_file
    #else 

    #end if

    #if $read.end=="single-end"
      $in 
    #else if $read.end=="paired-end"
      $in1 $in2
    #else
      
    #end if
  </command>

  <inputs>
    <conditional name="reference">
      <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?">
        <option value="indexed">Use a built-in genome index</option>
        <option value="history">Use a genome from the history and build index</option>
      </param>
      <when value="indexed">
        <param name="index" type="select" label="Select reference genome">
          <options from_data_table="bsfcall_indexes">
            <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="own_file" type="data" format="fasta" label="Select reference genome"/>
      </when>
    </conditional>

    <conditional name="read">
      <param name="end" type="select" label="Will you use single-end reads or paired-end reads?">
        <option value="single-end">Single-end reads</option>
        <option value="paired-end">Paired-end reads</option>
      </param>
      <when value="single-end">
        <param name="in" type="data" format="fastqsanger" label="Single-end reads in fastqsanger format"/>
      </when>
      <when value="paired-end">
        <param name="in1" type="data" format="fastqsanger" label="Paired-end reads 1 in fastqsanger format"/>
        <param name="in2" type="data" format="fastqsanger" label="Paired-end reads 2 in fastqsanger format"/>
      </when>
    </conditional> 
  </inputs>

  <outputs>
    <data name="outres" format="tabular" label="${tool.name} on ${on_string}: result" from_work_dir="bsf-call.out"/>
    <data name="outlog" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="bsfwork/bsf-call.log"/>
  </outputs>

  <help>
**bsf-call**

Mapping bisulfite-seq reads and calling methylated cytosines

------

**Input format**

Inputs are bisulfite-seq reads in fastqsanger format (single-end or paired-end), and a reference genome index (built-in or constructed from your fasta file). 

------

**Output format**

Output is a six-column tab-delimited file::

  Col.| Description
  ----+--------------------------------------
  1   | chromosome label (e.g. chr1)
  2   | genomic position (0-based)
  3   | strand (+,-)
  4   | mC context (CG, CHG, CHH)
  5   | mC rate (float)
  6   | read coverage

------

**Contact**

Toutai Mituyama

mituyama-toutai AT aist.go.jp
  </help>

  <citations>
    <citation type="doi">10.1093/nar/gkt1373</citation>
  </citations>

</tool>