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annotate shuffling.xml @ 0:24e4f42410e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
author iuc
date Mon, 11 May 2015 22:46:54 -0400
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children e8401372796a
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24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
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1 <tool id="vsearch_shuffling" name="VSearch shuffling" version="@VERSION@.0">
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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2 <description></description>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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3 <macros>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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4 <import>vsearch_macros.xml</import>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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5 </macros>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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6 <expand macro="requirements" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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7 <expand macro="stdio" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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8 <expand macro="version_command" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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9 <command>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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10 <![CDATA[
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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11 vsearch
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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12 @GENERAL@
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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13 --output $outfile
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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14 --seed $seed
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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15 --shuffle $infile
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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16 --topn $topn
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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17 ]]>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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18 </command>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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19 <inputs>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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20 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--shuffle)" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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21 <param name="seed" type="integer" value="0" label="Seed"
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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22 help="Zero to use random data source. (--seed)"/>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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23 <expand macro="topn" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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24 </inputs>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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25 <outputs>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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26 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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27 </outputs>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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28 <tests>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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29 <test>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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30 <param name="infile" value="db.fasta" ftype="fasta" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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31 <param name="seed" value="1"/>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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32 <param name="topn" value="5"/>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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33 <output name="outfile" file="shuffling_result1.fasta" ftype="fasta" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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34 </test>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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35 </tests>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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36 <help>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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37 <![CDATA[
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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38 **What it does**
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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39
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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40 Sequence shuffling to obtain new random sequences.
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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41
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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42 Shuffling options
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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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)
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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45 --shuffle FILENAME shuffle order of sequences pseudo-randomly
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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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>