<tool id="agile_wrapper" name="AGILE" version="1.0.0">
  <description> Quickly match reads to a reference genome or sequence file</description>
  <command interpreter="python">
    #if $source.source_select=="database" #agile_wrapper.py 0 $source.dbkey $input_query $output1 $max_sims $tile_size $max_freq $out_type $all
    #else                                 #agile_wrapper.py 1 $source.input_target $input_query $output1 $max_sims $tile_size $max_freq $out_type $all
    #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" label="Reference sequence" />
 		</when>
	</conditional>	
		<param name="input_query" type="data" format="fasta" label="Query sequences file"/>
		<param name="max_sims" type="integer" size="15" value="7" label="Maximum number of Single Imperfect Matches (SIMs) allowed as percentage of read length (-maxSIMs, default 7)" />
		<param name="tile_size" type="integer" size="15" value="20" label="Sets the length of tuples for creating hash table (-tileSize, default 20)" help="Usually between 11 and 20."/>
		<param name="max_freq" type="integer" size="15" value="8" label="Maximum number of occurrences of a pattern (k-tupple) allowed (-maxFreq, default 8"/>
		<param name="all" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output all matches? (-all, default true for MHC)"/>
		<param name="out_type" type="select" label="Output Format (-out default pslx for MHC">
				<option value="pslx">pslx</option>
				<option value="psl">psl</option>
				<option value="axt">axt</option>
				<option value="maf">maf</option>
				<option value="sim4">sim4</option>
				<option value="wublast">wublast</option>				
				<option value="blast">blast</option>
				<option value="blast8">blast8</option>
				<option value="blast9">blast9</option>
		</param>
	</inputs>
	<outputs>
		<data name="output1" format="tabular"/>
	</outputs>
	<requirements>
	    <requirement type="binary">agile</requirement>
	</requirements>
	<help>
	
.. class:: warningmark 

The default parameter values can be altered in the agile tool xml file

-----
	
**What it does**
 
This tool uses the **AGILE** alignment program, a faster replacement for the **BLAT** algorithm. Your reads file is searched against a genome build or another uploaded file. 

-----

**Parameters**

- *Maximum Single Imperfect Matches* (**-maxSIMs**) : The number of allowable mismatches as a percentage of read length.

- *Tuple Length* (**-tileSize**) : The length of tuples for craring a hash table.

- *Maximum Frequency* (**-maxFreq**) : The maximum number of pattern occurrences allowed.

- *All Matches* (**-all**) : Output all matches satisfying the match criteria (true/false).

- *Output Format* (**-out**) : Define the output format for the match file.

-----

**Reference**
 
 **AGILE**: Sanchit Misra, Ankit Agrawal, Wei-keng Liao, Alok Choudhary. Anatomy of a Hash-based Long Read Sequence Mapping Algorithm for Next Generation DNA Sequencing. Bioinformatics 2010; doi: 10.1093/bioinformatics/btq648.


	</help>
</tool>