<tool id="rmapq_wrapper" name="RMAPQ" version="1.0.0">
    <description>for Solexa Short Reads Alignment with Quality Scores</description>
    <command interpreter="python">
    #if $trim.choice=="No": #rmapq_wrapper.py $database $input_seq $input_score $high_score $high_len 0 $align_len $mismatch $output1
    #else: #rmapq_wrapper.py $database $input_seq $input_score $high_score $high_len $trim.read_len $align_len $mismatch $output1
    #end if
    </command>
    <inputs>
        <param name="database" type="select" display="radio" label="Target database">
			<options from_file="faseq.loc">
			  <column name="name" index="0"/>
			  <column name="value" index="0"/>
			</options>
        </param>
        <param name="input_seq" type="data" format="fasta" label="Sequence file"/>
        <param name="input_score" type="data" format="qualsolexa" label="Quality score file"/>
        <param name="high_score" type="float" size="15" value="40" label="Minimum score for high-quality base (-q)"/>
        <param name="high_len" type="integer" size="15" value="36" label="Minimal high-quality bases (-M)"/>
        <param name="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed"/>
        <param name="mismatch" type="select" label="Number of mismatches allowed (-m)">
            <option value="0">0</option>
            <option value="1">1</option>
            <option value="3">3</option>
            <option value="5">5</option>
        </param>
        <conditional name="trim">
            <param name="choice" type="select" label="To trim the reads">
                <option value="No">No</option>
                <option value="Yes">Yes</option>
            </param>
            <when value="No">
            </when>
            <when value="Yes">
                <param name="read_len" type="integer" size="15" value="36" label="Read length (-w)" /> 
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output1" format="bed"/>
    </outputs>
    <requirements>
      <requirement type="binary">rmapq</requirement>
    </requirements>
    <!-- 
    <tests>
        <test>
            <param name="database" value="/galaxy/data/faseq/test" />
            <param name="input_seq" value="rmapq_wrapper_test1.fasta" ftype="fasta"/>
            <param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qualsolexa" />
            <param name="high_score" value="40" />
            <param name="high_len" value="36" />
            <param name="read_len" value="36" />
            <param name="align_len" value="36" />
            <param name="mismatch" value="3" />
            <output name="output1" file="rmapq_wrapper_test1.bed"/> 
        </test>
    </tests>
    -->
    <help>
    
.. class:: warningmark

 RMAPQ was developed for **Solexa** reads. 

.. class:: infomark

**TIP**. The tool will guess the length of the reads, however, if you select to trim the reads, the *Maximal Length of the Reads* must be between 20 and 64. Reads with lengths longer than the specified value will be trimmed at the 3'end. 

-----

**What it does**

This tool runs **rmapq** (for more information, please see the reference below), searching against a genome build with sequence qualities.   

-----

**Parameters**

- *Minimal High-quality Bases* (**-M**): the minimal length of the high quality score bases
- *Minimum Score for High-quality Base* (**-q**) : the minimal quality score 
- *Minimal Length of a Hit* (**-h**) : the minimal length of an exact match or seed  
- *Number of Mismatches Allowed* (**-m**) : the maximal number of mismatches allowed in an alignment
- *Read Length* (**-w**) : maximal length of the reads; reads longer than the threshold will be truncated at 3' end.

-----

**Reference**

 **RMAP** is developed by Dr. Andrew D Smith and Dr. Zhenyu Xuan at the Cold Spring Harbor Laboratory. Please see http://rulai.cshl.edu/rmap/

    </help>
</tool>