Mercurial > repos > iuc > vsearch
annotate shuffling.xml @ 4:576963db5f1b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
| author | iuc |
|---|---|
| date | Fri, 20 Jan 2017 03:39:22 -0500 |
| parents | 4258854759ba |
| children |
| rev | line source |
|---|---|
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4258854759ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents:
2
diff
changeset
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1 <tool id="vsearch_shuffling" name="VSearch shuffling" version="@VERSION@.0"> |
| 0 | 2 <description></description> |
| 3 <macros> | |
| 4 <import>vsearch_macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <expand macro="version_command" /> | |
| 9 <command> | |
| 10 <![CDATA[ | |
| 11 vsearch | |
| 12 @GENERAL@ | |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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13 --output "$outfile" |
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3
4258854759ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents:
2
diff
changeset
|
14 --randseed "$randseed" |
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2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
|
15 --shuffle "$infile" |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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16 #if str( $topn ): |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
|
17 --topn "$topn" |
|
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
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18 #end if |
| 0 | 19 ]]> |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--shuffle)" /> | |
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3
4258854759ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents:
2
diff
changeset
|
23 <param argument="--randseed" type="integer" value="0" label="Seed" |
|
4258854759ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents:
2
diff
changeset
|
24 help="Zero to use random data source."/> |
| 0 | 25 <expand macro="topn" /> |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="infile" value="db.fasta" ftype="fasta" /> | |
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3
4258854759ba
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents:
2
diff
changeset
|
33 <param name="randseed" value="1"/> |
| 0 | 34 <param name="topn" value="5"/> |
| 35 <output name="outfile" file="shuffling_result1.fasta" ftype="fasta" /> | |
| 36 </test> | |
| 37 </tests> | |
| 38 <help> | |
| 39 <![CDATA[ | |
| 40 **What it does** | |
| 41 | |
| 42 Sequence shuffling to obtain new random sequences. | |
| 43 | |
| 44 Shuffling options | |
| 45 --output FILENAME output to specified FASTA file | |
| 46 --seed INT seed for PRNG, zero to use random data source (0) | |
| 47 --shuffle FILENAME shuffle order of sequences pseudo-randomly | |
| 48 --topn INT output just first n sequences | |
| 49 | |
| 50 | |
| 51 @EXTERNAL_DOCUMENTATION@ | |
| 52 | |
| 53 | |
| 54 ]]> | |
| 55 </help> | |
| 56 <expand macro="citations" /> | |
| 57 </tool> |