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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>
+
+