<tool id="trim_reads" name="Select high quality segments" version="1.0.0">
<description>from short reads</description>

<command interpreter="python">
 short_reads_trim_seq.py $trim $length $output1 $input1 $input2 $sequencing_method_choice.input3
</command>
<inputs>
<page>
    <param name="input1" type="data" format="fasta,txtseq.zip" label="Reads" />
    <param name="input2" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality scores" />
	<param name="trim" type="integer" size="5" value="20" label="Minimal quality score" help="bases scoring below this value will trigger splitting"/>
    <param name="length" type="integer" size="5" value="100" label="Minimal length of contiguous segment" help="report all high quality segments above this length. Setting this option to '0' will cause the program to return a single longest run of high quality bases per read" />
    <conditional name="sequencing_method_choice">
        <param name="sequencer" type="select" label="Select technology">
            <option value="454">Roche (454) or ABI SOLiD</option>
            <option value="Solexa">Illumina (Solexa)</option>
        </param>
        <when value="454">
            <param name="input3" type="select" label="Low quality bases in homopolymers" help="if set to 'DO NOT trigger splitting' the program will not count low quality bases that are within or adjacent to homonucleotide runs.  This will significantly reduce fragmentation of 454 data">
                <option value="yes">DO NOT trigger splitting </option>
                <option value="no">trigger splitting</option>
            </param>
        </when>
        <when value="Solexa">
            <param name="input3" type="integer" size="5" value="0" label="Restrict length of each read to" help="('0' = do not trim) The quality of Solexa reads drops towards the end. This option allows selecting the specified number of nucleotides from the beginning and then running the tool." />
        </when> 
    </conditional>
</page>
</inputs>

<outputs>
    <data name="output1" format="fasta" />
</outputs>

<tests>
	<test>
		<param name="sequencer" value="454" />
		<param name="input1" value="454.fasta" ftype="fasta" />
		<param name="input2" value="454.qual" ftype="qual454" />
		<param name="input3" value="no" />
		<param name="trim" value="20" />
		<param name="length" value="0" />
		<output name="output1" file="short_reads_trim_seq_out1.fasta" />
	</test>
	<test>
		<param name="sequencer" value="Solexa" />
		<param name="input1" value="solexa.fasta" ftype="fasta" />
		<param name="input2" value="solexa.qual" ftype="qualsolexa" />
		<param name="input3" value="0" />
		<param name="trim" value="20" />
		<param name="length" value="0" />
		<output name="output1" file="short_reads_trim_seq_out2.fasta" />
	</test>
</tests>

<help>
  
.. class:: warningmark

 To use this tool your quality score dataset needs to be in *Quality Score* format. Click pencil icon next to your dataset to set datatype to *Quality Score*.
 
-----

**What it does**

This tool finds high quality segments within sequencing reads generated by by Roche (454), Illumina (Solexa), or ABI SOLiD machines.

-----

**Example**


Suppose this is your sequencing read::
  
   5'---------*-------------*------**----3'
   
where **dashes** (-) are HIGH quality bases (above 20) and **asterisks** (*) are LOW quality bases (below 20). If the **Minimal length of contiguous segment** is set to **5** (of course, only for the purposes of this example), the tool will return::

   5'---------
               -------------
                             -------

you can see that the tool simply splits the read on low quality bases and then returns all segments longer than 5.  **Note**, that the output of this tool will likely contain higher number of shorter sequences compared to the original input.   If we set the **Minimal length of contiguous segment** to **0**, the tool will only return the single longest segment::

               -------------
               

               



</help>
</tool>