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1 <tool id="gsnap" name="gsnap">
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2
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3 <description>GSNAP version 2012-12-20.
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4 GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and
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5 GSNAP: Genomic Short-read Nucleotide Alignment Program
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6 </description>
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7
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8 <requirements>
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9 <requirement type="package">gmap</requirement>
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10 </requirements>
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11
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12
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13 <command interpreter="python"> wrappGSNAP.py
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14 -d $genomeName -D $genomeName.files_path -k $kmer -i $inputFasta -q $inputFastq -A $outputFormat
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15
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16 #if $optionPairedEnd.paire == 'Yes':
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17 -p $optionPairedEnd.pairedEndFile
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18 #end if
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19
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20 > $outputSam
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21
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22 </command>
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23
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24 <inputs>
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25 <param name="inputFasta" type="data" format="fasta" label="Reference genome file, fasta format."/>
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26 <param name="genomeName" type="text" value="Arabidopsis_Thaliana" label="Please give the reference genome a name! (Ex. Arabidopsis_Thaliana)"/>
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27 <param name="kmer" type="integer" value="12" label="Choose kmer value (<=16), a big kmer value can take more RAM(4Go)." />
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28 <param name="inputFastq" type="data" format="fastq" label="Input fastq file."/>
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29 <param name="outputFormat" type="text" format="sam" label="Choose an output format [sam, goby (need to re-compile with appropriate options)]."/>
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30
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31 <conditional name="optionPairedEnd">
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32 <param name="paire" type="select" label="pairedEnd fastq file">
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33 <option value="Yes">Yes</option>
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34 <option value="No" selected="true">No</option>
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35 </param>
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36 <when value="Yes">
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37 <param name="pairedEndFile" type="data" format="fastq"/>
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38 </when>
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39 <when value="No">
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40 </when>
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41 </conditional>
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42
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43 </inputs>
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44
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45 <outputs>
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46 <data format="sam" name="outputSam" label="gsnap Output"/>
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47 </outputs>
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48
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49 </tool>
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