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<tool id="quikr" name="Quikr">
<description>Classify with Quikr</description>
<command>quikr -v -k $kmer -s $db -i $input -o $output</command>
<inputs>
<param name="input" type="data" format="fasta" label="input fasta"/>
<param name="db" type="data" format="data" label="trained database"/>
<param name="lambda" type="integer" size="6" value="10000" label="lambda" help="default 10000"/>
<param name="kmer" type="integer" size="2" value="6" label="What mer size to use?" help="range 6 - 12"/>
</inputs>
<outputs>
<data name="output" format="tabular"/>
</outputs>
<help>
**What it does**
This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
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**Example**
Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
>EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
>EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
Running this tool while setting **How many characters to keep?** to **14** will produce this::
EYKX4VC02EQLO5 108
EYKX4VC02D4GS2 60
</help>
</tool>
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