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1 <tool id="vsearch_shuffling" name="VSearch shuffling" version="@VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>vsearch_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
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11 vsearch
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12 @GENERAL@
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13 --output $outfile
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14 --seed $seed
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15 --shuffle $infile
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16 --topn $topn
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--shuffle)" />
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21 <param name="seed" type="integer" value="0" label="Seed"
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22 help="Zero to use random data source. (--seed)"/>
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23 <expand macro="topn" />
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24 </inputs>
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25 <outputs>
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26 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="infile" value="db.fasta" ftype="fasta" />
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31 <param name="seed" value="1"/>
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32 <param name="topn" value="5"/>
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33 <output name="outfile" file="shuffling_result1.fasta" ftype="fasta" />
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34 </test>
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35 </tests>
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36 <help>
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37 <![CDATA[
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38 **What it does**
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39
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40 Sequence shuffling to obtain new random sequences.
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41
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42 Shuffling options
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43 --output FILENAME output to specified FASTA file
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44 --seed INT seed for PRNG, zero to use random data source (0)
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45 --shuffle FILENAME shuffle order of sequences pseudo-randomly
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46 --topn INT output just first n sequences
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47
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48
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49 @EXTERNAL_DOCUMENTATION@
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50
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51 -------
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52
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53 @REFERENCES@
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54
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55
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56 ]]>
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57 </help>
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58 <expand macro="citations" />
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59 </tool>
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