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annotate shuffling.xml @ 10:32e8ed5c6100 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb"
author iuc
date Wed, 04 Nov 2020 07:35:42 +0000
parents 50cc0d99b800
children
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50cc0d99b800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit b'29f6e6424a37947adbe1eba92f0e7d3c83efc042'
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1 <tool id="vsearch_shuffling" name="VSearch shuffling" version="@VERSION@.0">
0
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2 <description></description>
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3 <macros>
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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>
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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[
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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11 vsearch
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12 @GENERAL@
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13 --output "$outfile"
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14 --randseed "$randseed"
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15 --shuffle "$infile"
e8401372796a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
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16 #if str( $topn ):
e8401372796a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
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17 --topn "$topn"
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18 #end if
0
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--shuffle)" />
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23 <param argument="--randseed" type="integer" value="0" label="Seed"
50cc0d99b800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit b'29f6e6424a37947adbe1eba92f0e7d3c83efc042'
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24 help="Zero to use random data source."/>
0
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25 <expand macro="topn" />
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26 </inputs>
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27 <outputs>
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28 <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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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="infile" value="db.fasta" ftype="fasta" />
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50cc0d99b800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit b'29f6e6424a37947adbe1eba92f0e7d3c83efc042'
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33 <param name="randseed" value="1"/>
0
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34 <param name="topn" value="5"/>
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35 <output name="outfile" file="shuffling_result1.fasta" ftype="fasta" />
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36 </test>
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37 </tests>
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38 <help>
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39 <![CDATA[
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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40 **What it does**
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42 Sequence shuffling to obtain new random sequences.
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44 Shuffling options
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45 --output FILENAME output to specified FASTA file
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46 --seed INT seed for PRNG, zero to use random data source (0)
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47 --shuffle FILENAME shuffle order of sequences pseudo-randomly
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48 --topn INT output just first n sequences
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51 @EXTERNAL_DOCUMENTATION@
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52
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54 ]]>
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55 </help>
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56 <expand macro="citations" />
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57 </tool>