<tool id="maq_cs_wrapper" name="MAQ for SOLiD" version="1.0.0">
    <description> </description>
    <command>
python '$__tool_directory__/maq_cs_wrapper.py'
'$output1'
'$output2'
'$ref'
'$library_type.f3_reads'
'$library_type.f3_qual'
$library_type.is_paired
#if $library_type.is_paired == "yes":
    '$library_type.r3_reads'
    '$library_type.r3_qual'
#else:
    "None"
    "None"
#end if
$min_mapqual
$max_mismatch
'$output3'
    </command>

    <inputs>
        <param name="ref" type="data" format="fasta" label="Target Genome"/>
        <conditional name="library_type">
          <param name="is_paired" type="select" label="Is the library mate-paired?" multiple="false">
             <option value="no">No</option>
             <option value="yes">Yes</option>
         </param>
         <when value="no">
           <param name="f3_reads" type="data" format="csfasta" label="F3 reads file"/>
           <param name="f3_qual" type="data" format="qualsolid" label="F3 quality file" help="If your dataset doesn't show up in the menu, click the pencil icon next to your dataset and set the datatype to 'qualsolid'" />
          </when>
          <when value="yes">
           <param name="f3_reads" type="data" format="csfasta" label="F3 reads file"/>
           <param name="f3_qual" type="data" format="qualsolid" label="F3 quality file" help="If your dataset doesn't show up in the menu, click the pencil icon next to your dataset and set the datatype to 'qualsolid'" />
           <param name="r3_reads" type="data" format="csfasta" label="R3 reads file"/>
           <param name="r3_qual" type="data" format="qualsolid" label="R3 quality file" help="If your dataset doesn't show up in the menu, click the pencil icon next to your dataset and set the datatype to 'qualsolid'" />
          </when>
      </conditional>
      <param name="min_mapqual" type="integer" value="0" label="Minimum mapping quality allowed for a read to be used" help="Reads below the specified mapping quality will not be considered in coverage and SNP analysis."/>
      <param name="max_mismatch" type="integer" value="7" label="Maximum number of mismatches allowed for a read to be used" help="Reads above the specified threshold will not be considered in coverage and SNP analysis."/>
    </inputs>
    <outputs>
        <data name="output1" format="tabular" metadata_source="ref" />
        <data name="output2" format="tabular" metadata_source="ref" />
        <data name="output3" format="customtrack" metadata_source="ref" />
    </outputs>
    <!--  "ToolTestCase does not deal with multiple outputs properly yet."
    <tests>
        <test>
            <param name="ref" value="phiX_mod.fasta" />
            <param name="is_paired" value="no" />
            <param name="f3_reads" value="phiX_solid.csfasta" />
            <param name="f3_qual" value="phiX_solid.qualsolid" />
            <param name="min_mapqual" value="0" />
            <param name="max_mismatch" value="7" />
            <output name="output1" file="phiX_solid_maq.map" />
            <output name="output2" file="phiX_solid_maq.pileup" />
            <output name="output3" file="phiX_solid_maq.ctrack" />
        </test>
    </tests>
    -->
<help>
.. class:: infomark

**What it does**

This tool maps SOLiD color-space reads against the target genome using MAQ. It produces three output datasets:


**ALIGNMENT INFO** : contains the read alignment information,

**PILEUP** : contains the coverage and SNP statistics for every nucleotide of the target genome,

**CUSTOM TRACK** : contains the coverage and SNP statistics as custom tracks displayable in the UCSC browser.

-----

**The ALIGNMENT INFO dataset will contain the following fields:**

* column 1  = read name
* column 2  = chromosome
* column 3  = position
* column 4  = strand
* column 5  = insert size from the outer coorniates of a pair
* column 6  = paired flag
* column 7  = mapping quality
* column 8  = single-end mapping quality
* column 9  = alternative mapping quality
* column 10 = number of mismatches of the best hit
* column 11 = sum of qualities of mismatched bases of the best hit
* column 12 = number of 0-mismatch hits of the first 24bp
* column 13 = number of 1-mismatch hits of the first 24bp on the reference
* column 14 = length of the read
* column 15 = read sequence
* column 16 = read quality


**The PILEUP dataset will contain the following fields:**

* column 1  = chromosome
* column 2  = position
* column 3  = reference nucleotide
* column 4  = coverage (number of reads that cover this position)
* column 5  = number of SNPs
* column 6  = number of As
* column 7  = number of Ts
* column 8  = number of Gs
* column 9  = number of Cs
  </help>
  <code file="maq_cs_wrapper_code.py"/>
</tool>