Mercurial > repos > iuc > vsearch
annotate shuffling.xml @ 5:e8401372796a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
| author | iuc |
|---|---|
| date | Thu, 17 Dec 2015 12:51:04 -0500 |
| parents | 24e4f42410e5 |
| children | 50cc0d99b800 |
| rev | line source |
|---|---|
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5
e8401372796a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
iuc
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1 <tool id="vsearch_shuffling" name="VSearch shuffling" version="@VERSION@.1"> |
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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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2 <description></description> |
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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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3 <macros> |
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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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changeset
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4 <import>vsearch_macros.xml</import> |
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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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changeset
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5 </macros> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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6 <expand macro="requirements" /> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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7 <expand macro="stdio" /> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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8 <expand macro="version_command" /> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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9 <command> |
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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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diff
changeset
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10 <![CDATA[ |
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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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changeset
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11 vsearch |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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changeset
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12 @GENERAL@ |
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5
e8401372796a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
iuc
parents:
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13 --output "$outfile" |
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e8401372796a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
iuc
parents:
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diff
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14 --seed "$seed" |
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e8401372796a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
iuc
parents:
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diff
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15 --shuffle "$infile" |
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e8401372796a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
iuc
parents:
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16 #if str( $topn ): |
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e8401372796a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
iuc
parents:
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diff
changeset
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17 --topn "$topn" |
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e8401372796a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
iuc
parents:
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18 #end if |
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0
24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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19 ]]> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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changeset
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20 </command> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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21 <inputs> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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22 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--shuffle)" /> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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23 <param name="seed" type="integer" value="0" label="Seed" |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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changeset
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24 help="Zero to use random data source. (--seed)"/> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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25 <expand macro="topn" /> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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26 </inputs> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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27 <outputs> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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28 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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29 </outputs> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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30 <tests> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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31 <test> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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32 <param name="infile" value="db.fasta" ftype="fasta" /> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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33 <param name="seed" value="1"/> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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34 <param name="topn" value="5"/> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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35 <output name="outfile" file="shuffling_result1.fasta" ftype="fasta" /> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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36 </test> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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changeset
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37 </tests> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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changeset
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38 <help> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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39 <![CDATA[ |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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40 **What it does** |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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41 |
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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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42 Sequence shuffling to obtain new random sequences. |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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43 |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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44 Shuffling options |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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changeset
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45 --output FILENAME output to specified FASTA file |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff
changeset
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46 --seed INT seed for PRNG, zero to use random data source (0) |
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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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47 --shuffle FILENAME shuffle order of sequences pseudo-randomly |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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48 --topn INT output just first n sequences |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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49 |
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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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50 |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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51 @EXTERNAL_DOCUMENTATION@ |
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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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52 |
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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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53 |
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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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54 ]]> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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55 </help> |
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24e4f42410e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
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56 <expand macro="citations" /> |
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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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57 </tool> |