<description>Determine number of reads in fastq(s) and if they are mate-pair</description>
<inputs>
<conditionalname="singlePaired">
<paramname="sPaired"type="select"label="Is this library mate-paired?">
<optionvalue="single">Single-end</option>
<optionvalue="paired">Paired-end</option>
<optionvalue="matePairs">MatePairs</option>
</param>
<whenvalue="single">
<paramname="sInput1"type="data"format="fastq"label="Single end illumina fastq file"optional="false"/>
</when>
<whenvalue="paired">
<paramname="pInput1"type="data"format="fastq,fastqsanger,fastqillumina,fastqsolexa"label="Forward FASTQ file"help="Must have ASCII encoded quality scores"/>
<paramname="pInput2"type="data"format="fastq,fastqsanger,fastqillumina,fastqsolexa"label="Reverse FASTQ file"help="File format must match the Forward FASTQ file"/>
</when>
<whenvalue="matePairs">
<paramname="mInput1"type="data"format="fastq,fastqsanger,fastqillumina,fastqsolexa"label="Forward FASTQ file"help="Must have ASCII encoded quality scores"/>
<paramname="mInput2"type="data"format="fastq,fastqsanger,fastqillumina,fastqsolexa"label="Reverse FASTQ file"help="File format must match the Forward FASTQ file"/>
<paramname="k"type="integer"value="13"label="K-mer size"help="Specifies the word length. [wordlen] is an integer within the limits. between 2 and less then 20. The default word length is 13"/>
<paramname="s"type="text"label="Stepsiz"help="Specifies how many bases are skipped between indexed words."/>
Generates an index of k-mer words for the genomic reference sequences. The words are of fixed length <wordlen> and are sampled at equidistant steps <stepsiz> bases apart. The reference sequences are provided in a single file <reference_file> in FASTA or FASTQ format. Two binary files are output. The file <index_name>.sma contains the reference sequences in compressed form. The file <index_name>.smi contains the k-mer word index.
------
Please cite the website "http://www.sanger.ac.uk/resources/software/smalt/".
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-k <wordlen>
Specifies the word length. <wordlen> is an integer within the limits
2 < wordlen <= 20. The default word length is 13.
-s <stepsiz>
Specifies how many bases are skipped between indexed words. With '-s 1'
every k-mer word along the reference sequences is indexed. With '-s 2'
every other word is indexed etc. By default the step size is set equal
<description>Sample insert size distribution for paired reads.</description>
<inputs>
<paramname="mInput1"type="data"format="fastq,fastqsanger,fastqillumina,fastqsolexa"label="Forward FASTQ file"help="Must have ASCII encoded quality scores"/>
<paramname="mInput2"type="data"format="fastq,fastqsanger,fastqillumina,fastqsolexa"label="Reverse FASTQ file"help="File format must match the Forward FASTQ file"/>
<paramname="threads"type="text"format="integer"value="2"label="Number of threads to use"help="The order of the reads in the input files is not preserved for the output unless '-O' is also specified"/>
<paramname="minscor"type="text"label="Sets an absolute threshold of the Smith-Waterman scores."help="Mappings with scores below that threshold will not be reported. The default is < minscor > = < wordlen > + < stepsiz > - 1"/>
<paramname="minbasq"type="text"label="Sets a base quality threshold (0 <= minbasq <= 10, default 0)"help="K-mer words of the read with nucleotides that have a base quality below this threshold are not looked up in the hash index."/>
<paramname="num_reads"type="integer"value="100"label="Map only every [num_reads]-th read pair"help="Default 100"/>