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<tool id="GeCoS" name="GeCoS" version="1.0.0">
	<description>(GeneCodonSearch) calculates the codon composition in a DNA sequence.</description>
	<command interpreter="python">GeneCodonSearch1_2.py -c $codon -m $minimum -i $input_sequences -r $resultfile</command>
	<inputs>
		<param type="data" format="fasta" name="input_sequences" label="Input Sequences"/>
		<param name="codon" type="select" label="Codons" multiple="true">
			<option value="ATA" selected="false">ATG</option>
			<option value="ATC" selected="false">ATC</option>
			<option value="ATT" selected="false">ATT</option>
			<option value="ATG" selected="false">ATG</option>
			<option value="ACA" selected="false">ACA</option>
			<option value="ACC" selected="false">ACC</option>
			<option value="ACG" selected="false">ACG</option>
			<option value="ACT" selected="false">ACT</option>
			<option value="AAC" selected="false">AAC</option>
			<option value="AAT" selected="false">AAT</option>
			<option value="AAA" selected="false">AAA</option>
			<option value="AAG" selected="false">AAG</option>
			<option value="AGC" selected="false">AGC</option>
			<option value="AGT" selected="false">AGT</option>
			<option value="AGA" selected="false">AGA</option>
			<option value="AGG" selected="false">AGG</option>
			<option value="CTA" selected="false">CTA</option>
			<option value="CTC" selected="false">CTC</option>
			<option value="CTG" selected="false">CTG</option>
			<option value="CTT" selected="false">CTT</option>
			<option value="CCA" selected="false">CCA</option>
			<option value="CCC" selected="false">CCC</option>
			<option value="CCG" selected="false">CCG</option>
			<option value="CCT" selected="false">CCT</option>
			<option value="CAC" selected="false">CAC</option>
			<option value="CAT" selected="false">CAT</option>
			<option value="CAA" selected="false">CAA</option>
			<option value="CAG" selected="false">CAG</option>
			<option value="CGA" selected="false">CGA</option>
			<option value="CGC" selected="false">CGC</option>
			<option value="CGG" selected="false">CGG</option>
			<option value="CGT" selected="false">CGT</option>
			<option value="GTA" selected="false">GTA</option>
			<option value="GTC" selected="false">GTC</option>
			<option value="GTG" selected="false">GTG</option>
			<option value="GTT" selected="false">GTT</option>
			<option value="GCA" selected="false">GCA</option>
			<option value="GCC" selected="false">GCC</option>
			<option value="GCG" selected="false">GCG</option>
			<option value="GCT" selected="false">GCT</option>
			<option value="GAC" selected="false">GAC</option>
			<option value="GAT" selected="false">GAT</option>
			<option value="GAA" selected="false">GAA</option>
			<option value="GAG" selected="false">GAG</option>
			<option value="GGA" selected="false">GGA</option>
			<option value="GGC" selected="false">GGC</option>
			<option value="GGG" selected="false">GGG</option>
			<option value="GGT" selected="false">GGT</option>
			<option value="TCA" selected="false">TCA</option>
			<option value="TCC" selected="false">TCC</option>
			<option value="TCG" selected="false">TCG</option>
			<option value="TCT" selected="false">TCT</option>
			<option value="TTC" selected="false">TTC</option>
			<option value="TTT" selected="false">TTT</option>
			<option value="TTA" selected="false">TTA</option>
			<option value="TTG" selected="false">TTG</option>
			<option value="TAC" selected="false">TAC</option>
			<option value="TAT" selected="false">TAT</option>
			<option value="TAA" selected="false">TAA</option>
			<option value="TAG" selected="false">TAG</option>
			<option value="TGC" selected="false">TGC</option>
			<option value="TGT" selected="false">TGT</option>
			<option value="TGA" selected="false">TGA</option>
			<option value="TGG" selected="false">TGG</option>
		</param>
		<param name="minimum" type="float" value="0.0" label="Minimum codon content (cutoff)"/>
	</inputs>
	<outputs>
		<data format="txt" name="resultfile"/>
	</outputs>

	<help>
	**What it does**
		**GeCos** is a tool that calculates the codon composition of any given DNA sequence. 

	**Input**

	- If more than one sequence is analyzed at a time, a **cutoff value** can be used to filter the output. Only the sequences with a higher total score than the cutoff value will be displayed in the output.

	- The DNA sequence(s), that are supposed to be analyzed with GeCoS need to be formatted as fasta. 
	
	Example::

	    &gt;CCE57618 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:166:1143:1 gene:HUS2011_pII0001 description:replication initiation protein RepFIB
	    GTGGATAAGTC ... TCTTCAAATCCCGCTGA
	    &gt;CCE57620 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:1422:2162:-1 gene:HUS2011_pII0003 description:site-specific recombinase
	    ATGAACAATG ... CTCCCCTGAAGTAA
	    &gt;CCE57621 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:2531:2692:-1 gene:HUS2011_pII0004 description:plasmid stabilisation system family protein
	    ATGAGTAATCA ... ATTTCAACTGA
	    &gt;CCE57622 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:2894:3076:-1 gene:HUS2011_pII0005 description:putative transcriptional regulator
	    ATGGCCAG ... AGAAGGCT

	**Output**

	- GeCoS produces a matrix containing the identifier used in the input, the combined score of the sequence and the number of each of the chosen codons.

	- **Total Score** = sum of codon occurences / sequence length * number of analyzed codons

	- The output is sorted from low to high (Total Score: 0 to 1).

	Example::

		[['Gene_ID' 'Total Score' 'AGG' 'AGC' 'CCC' 'TGC' 'GCG']
		['CCE57562' 0.0190476 1 3 1 2 1]
		['CCQ29559' 0.0190476 0 1 2 2 1]
		...
		['CCQ31238' 0.0328358 0 3 0 6 2]
		['CCE57539' 0.05 2 0 4 3 3]]

	</help>

</tool>