root/galaxy-central/tools/metag_tools/blat_wrapper.xml @ 2

<tool id="blat_wrapper" name="BLAT" version="1.0.0">
  <description> compare sequencing reads against UCSC genome builds</description>
  <command interpreter="python">
    #if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off
    #else                                 #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off
    #end if# ${GALAXY_DATA_INDEX_DIR}
  </command>
        <inputs>
        <conditional name="source">
                <param name="source_select" type="select" label="Target source">
                                <option value="database">Genome Build</option>
                                <option value="input_ref">Your Upload File</option>
                </param>
                <when value="database">
                        <param name="dbkey" type="genomebuild" label="Genome" />
                </when>
                <when value="input_ref">
                        <param name="input_target" type="data" format="fasta" label="Reference sequence" />
                </when>
        </conditional>  
                <param name="input_query" type="data" format="fasta" label="Sequence file"/>
                <param name="iden" type="float" size="15" value="90.0" label="Minimal identity (-minIdentity)" />
                <param name="tile_size" type="integer" size="15" value="11" label="Minimal size of exact match (-tileSize)" help="Must be between 6 and 18."/>
                <param name="one_off" type="integer" size="15" value="0" label="Number of mismatch in the word (-oneOff)" help="Must be between 0 and 2." />
        </inputs>
        <outputs>
                <data name="output1" format="tabular"/>
        </outputs>
        <requirements>
          <requirement type="binary">blat</requirement>
        </requirements>
        <tests>
                <test>
                <param name="source_select" value="database" />
                <param name="dbkey" value="eschColi_K12" />
                <param name="input_query" value="blat_wrapper_test1.fa" ftype="fasta"/>
                <param name="iden" value="90.0" />
                <param name="tile_size" value="11" />
                <param name="one_off" value="0" />
                <output name="output1" file="blat_wrapper_test1.out" />
                </test>
        </tests>
        <help>
        
.. class:: warningmark 

Using a smaller word size (*Minimal Size of Exact Match*) will increase the computational time.

.. class:: warningmark 

Using a larger mismatch number (*Number of Mismatch in the Word*) will increase the computational time.

-----
        
**What it does**
 
This tool currently uses the **BLAT** alignment program. Your short reads file is searched against a genome build or another uploaded file. 
 
-----
 
**Example**
 
- Input a multiple fasta file::

        &gt;seq1
        TGGTAATGGTGGTTTTTTTTTTTTTTTTTTATTTTT

- Use the default settings:

  - alignment identity must be higher than or equal to 90%.
  
  - minimal size of exact match to trigger an alignment is 11.
  
  - allow 0 mismatches in the above exact match size.
  
- Search against ce2 (C. elegans March 2004), partial result::

        25 1 0 0 0 0 0 0 + seq1 36 10 36 chrI 15080483 9704438 9704464 1 26, 10, 9704438, ggttttttttttttttttttattttt, ggtttttttttttttttttttttttt,
        27 0 0 0 0 0 1 32 + seq1 36 9 36 chrI 15080483 1302536 1302595 2 21,6, 9,30, 1302536,1302589, tggtttttttttttttttttt,attttt, tggtttttttttttttttttt,attttt,

-----

**Parameters**

- *Minimal Identity* (**-minIdentity**) : In percent, the minimum sequence identity between the query and target alignment. Default is 90.

- *Minimal Size of Exact Match* (**-tileSize**) : The size of a match that will trigger an alignment. Default is 11. Usually between 8 and 12. Must be between 6 and 18.

- *Number of Mismatch in the Word* (**-oneOff**) : The number of mismatches allowed in the word (tile size) and still triggers an alignment. Default is 0.

-----

**Reference**
 
 **BLAT**: Kent, W James, BLAT--the BLAST-like alignment tool. (2002) Genome Research:12(4) 656-664.


        </help>
</tool>