<tool id="solid2fastq" name="Convert">
  <description>SOLiD output to fastq</description>
  <command interpreter="python">
    #if   $is_run.paired == "no"    #solid2fastq.py --fr=$input1 --fq=$input2 --fout=$out_file1 -q $qual $trim_name $trim_first_base $double_encode
    #elif $is_run.paired == "yes"   #solid2fastq.py --fr=$input1 --fq=$input2 --fout=$out_file1 --rr=$input3 --rq=$input4 --rout=$out_file2 -q $qual $trim_name $trim_first_base $double_encode
    #end if#
  </command>
  <inputs>
    <param name="input1" type="data" format="csfasta" label="Select reads"/>
    <param name="input2" type="data" format="qualsolid" label="Select qualities"/>
    <conditional name="is_run">
        <param name="paired" type="select" label="Is this a mate-pair run?">
            <option value="no" selected="true">No</option>
            <option value="yes">Yes</option>
        </param>
        <when value="yes">
            <param name="input3" type="data" format="csfasta" label="Select Reverse reads"/>
            <param name="input4" type="data" format="qualsolid" label="Select Reverse qualities"/>
        </when>
        <when value="no">
        </when>
    </conditional>
    <param name="qual" label="Remove reads containing color qualities below this value" type="integer" value="0"/>
    <param name="trim_name" type="select" label="Trim trailing &quot;_F3&quot; and &quot;_R3&quot; ?">
        <option value="-t" selected="true">Yes</option>
        <option value="">No</option>
    </param>
    <param name="trim_first_base" type="select" label="Trim first base?">
        <option value="-f">Yes (BWA)</option>
        <option value="" selected="true">No (bowtie)</option>
    </param>
    <param name="double_encode" type="select" label="Double encode?">
        <option value="-d">Yes (BWA)</option>
        <option value="" selected="true">No (bowtie)</option>
    </param>
  </inputs>
  <outputs>
    <data format="fastqcssanger" name="out_file1"/>
    <data format="fastqcssanger" name="out_file2">
        <filter>is_run['paired'] == 'yes'</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input1" value="fr.csfasta" ftype="csfasta"/>
      <param name="input2" value="fr.qualsolid" ftype="qualsolid" />
      <param name="paired" value="no"/>
      <param name="qual" value="0" />
      <param name="trim_first_base" value="No" />
      <param name="trim_name" value="No" />
      <param name="double_encode" value="No"/>
      <output name="out_file1" file="solid2fastq_out_1.fastq"/>
    </test>
    <test>
      <param name="input1" value="fr.csfasta" ftype="csfasta"/>
      <param name="input2" value="fr.qualsolid" ftype="qualsolid" />
      <param name="paired" value="yes"/>
      <param name="input3" value="rr.csfasta" ftype="csfasta"/>
      <param name="input4" value="rr.qualsolid" ftype="qualsolid" />
      <param name="qual" value="0" />
      <param name="trim_first_base" value="No" />
      <param name="trim_name" value="Yes" />
      <param name="double_encode" value="No"/>
      <output name="out_file1" file="solid2fastq_out_2.fastq"/>
      <output name="out_file2" file="solid2fastq_out_3.fastq"/>
    </test>
 </tests>
<help>
**What it does**

Converts output of SOLiD instrument (versions 3.5 and earlier) to fastq format suitable for bowtie, bwa, and PerM mappers.

--------

**Input datasets**

Below are examples of forward (F3) reads and quality scores:

Reads::

    &gt;1831_573_1004_F3
    T00030133312212111300011021310132222
    &gt;1831_573_1567_F3
    T03330322230322112131010221102122113

Quality scores::

    &gt;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
    &gt;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


**Mate pairs**

If your data is from a mate-paired run, you will have additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with "_R3".
In this case choose **Yes** from the *Is this a mate-pair run?* drop down and you will be able to select R reads. When processing mate pairs this tool generates two output files: one for F3 reads and the other for R3 reads.
The reads are guaranteed to be paired -- mated reads will be in the same position in F3 and R3 fastq file. However, because pairing is verified it may take a while to process an entire SOLiD run (several hours).

------

**Explanation of parameters**

**Remove reads containing color qualities below this value** - any read that contains as least one color call with quality lower than the specified value **will not** be reported.

**Trim trailing "_F3" and "_R3"?** - does just that. Not necessary for bowtie. Required for BWA.

**Trim first base?** - SOLiD reads contain an adapter base such as the first T in this read::

    &gt;1831_573_1004_F3
    T00030133312212111300011021310132222
  
this option removes this base leaving only color calls. Not necessary for bowtie. Required for BWA.

**Double encode?** - converts color calls (0123.) to pseudo-nucleotides (ACGTN). Not necessary for bowtie. Required for BWA.

------

**Examples of output**

When all parameters are left "as-is" you will get this (using reads and qualities shown above)::

 @1831_573_1004
 T00030133312212111300011021310132222
 +
 %%&gt;CCAA9952+C&gt;5C.?C79,=42C292:C(9/-7
 @1831_573_1004
 T03330322230322112131010221102122113
 +
 );@@17?@=&gt;7??@A8?==@4A?A4)A+.'A+'1,

Setting *Trim first base from reads* to **Yes** will produce this::

 @1831_573_1004
 00030133312212111300011021310132222
 +
 %%&gt;CCAA9952+C&gt;5C.?C79,=42C292:C(9/-7
 @1831_573_1004
 03330322230322112131010221102122113
 +
 );@@17?@=&gt;7??@A8?==@4A?A4)A+.'A+'1,

Finally, setting *Double encode* to **Yes** will yield::

 @1831_573_1004
 TAAATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
 +
 %%&gt;CCAA9952+C&gt;5C.?C79,=42C292:C(9/-7
 @1831_573_1004
 TATTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
 +
 );@@17?@=&gt;7??@A8?==@4A?A4)A+.'A+'1,
</help>
</tool>