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<tool id="countspersequence" name="Kmer Counts Per Sequence">
<description>get kmer counts for each sequence</description>
<command>
kmer_counts_per_sequence
-k $kmer
#if labels:
-l
#endif
#if $reverse:
-c
#endif
#if $sparse:
-s
#endif
-i $input > $output
</command>
<inputs>
<param name="input" type="data" format="fasta" label="input fasta file"/>
<param name="kmer" type="integer" size="2" value="6" label="What mer size to use?" help="range 1 - 30"/>
<param name="labels" type="boolean" value="True" label="do you want mer labels (AAA, AAC, AAG) shown?" help="" />
<param name="reverse" type="boolean" value="True" label="do you want to count both strands (the reverse compliment)?" help="" />
<param name="sparse" type="boolean" value="True" label="do you want to output only nonzero counts?"help="" />
</inputs>
<outputs>
<data name="output" format="tabular"/>
</outputs>
<help>
input a sample file, get a count of kmers in each sequence
</help>
</tool>
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