<tool id="solid_to_fastq" name="SOLiD-to-FASTQ" version="1.0.0">
  <description>converts SOLiD data to FASTQ data</description>
  <command interpreter="python">
    solid_to_fastq.py 
    --input1=$input1 
    --input2=$input2
    #if $paired.pairedSingle == "single":
     --input3="None"
     --input4="None"
    #else:
     --input3=$input3
     --input4=$input4
    #end if
    --output1=$output1
    #if $paired.pairedSingle == "single":
     --output2="None"
    #else:
     --output2=$output2
    #end if
  </command>
  <inputs>
    <conditional name="paired">
      <param name="pairedSingle" type="select" label="Is this library mate-paired?">
        <option value="single">Single</option>
        <option value="paired">Paired</option>
      </param>
      <when value="single">
        <param name="input1" type="data" format="csfasta" label="F3 read file" />
        <param name="input2" type="data" format="qualsolid" label="F3 qual file" />
      </when>
      <when value="paired">
        <param name="input1" type="data" format="csfasta" label="F3 read file" />
        <param name="input2" type="data" format="qualsolid" label="F3 qual file" />
        <param name="input3" type="data" format="csfasta" label="R3 read file" />
        <param name="input4" type="data" format="qualsolid" label="R3 qual file" />      
      </when>
    </conditional>
  </inputs>
  <outputs>
    <!-- Variable number of outputs. Either one (for single-end) or two (for paired-end) -->
    <data name="output1" format="fastqsanger"/>
    <data name="output2" format="fastqsanger">
      <filter>paired['pairedSingle'] == 'paired'</filter>
    </data>    
  </outputs>
  <tests>
    <test>
      <param name="pairedSingle" value="single" />
      <param name="input1" value="s2fq_phiX.csfasta" ftype="csfasta" />
      <param name="input2" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
      <output name="output1" file="s2fq_out1.fastqsanger" />
    </test>
    <test>
      <param name="pairedSingle" value="paired" />
      <param name="input1" value="s2fq_paired_F3.csfasta" ftype="csfasta" />
      <param name="input2" value="s2fq_paired_F3_QV.qualsolid" ftype="qualsolid" />
      <param name="input3" value="s2fq_paired_R3.csfasta" ftype="csfasta" />
      <param name="input4" value="s2fq_paired_R3_QV.qualsolid" ftype="qualsolid" />
      <output name="output1" file="s2fq_out2.fastqsanger" />
      <!-- testing framework does not deal with multiple outputs yet
      <output name="output2" file="s2fq_out3.fastqsanger" />
      -->
    </test>
  </tests>
  <help>

**What it does**

This tool takes reads and quality files and converts them to FASTQ data ( Sanger variant ). Any -1 qualities are converted to 1 before being converted to FASTQ. Note that it also converts sequences to base pairs.

-----

**Example**

- Converting the following sequences::

    >1831_573_1004_F3
    T00030133312212111300011021310132222
    >1831_573_1567_F3
    T03330322230322112131010221102122113

- and quality scores::

    >1831_573_1004_F3
    4 29 34 34 32 32 24 24 20 17 10 34 29 20 34 13 30 34 22 24 11 28 19 17 34 17 24 17 25 34 7 24 14 12 22
    >1831_573_1567_F3
    8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 32 10 13 6 32 10 6 16 11

- will produce the following Sanger FASTQ data::

    @1831_573_1004/1
    AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
    +
    >CCAA9952+C>5C.?C79,=42C292:C(9/-7
    @1831_573_1567/1
    TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
    +
    ;@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,

    </help>
</tool>