Mercurial > repos > iuc > vsearch
annotate alignment.xml @ 2:f29e21388219 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
| author | iuc |
|---|---|
| date | Thu, 17 Dec 2015 12:53:39 -0500 |
| parents | fae6527990af |
| children | 4258854759ba |
| rev | line source |
|---|---|
|
2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
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changeset
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1 <tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.1"> |
| 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@ | |
| 13 $acceptall | |
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2
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
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changeset
|
14 --id "${id}" |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
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diff
changeset
|
15 --iddef "${iddef}" |
|
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
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changeset
|
16 --allpairs_global "${infile}" |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
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changeset
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17 --alnout "${outfile}" |
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f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
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0
diff
changeset
|
18 #if str( $query_cov ): |
|
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
|
19 --query_cov "${query_cov}" |
|
f29e21388219
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents:
0
diff
changeset
|
20 #end if |
| 0 | 21 @USERFIELDS@ |
| 22 ]]> | |
| 23 </command> | |
| 24 <inputs> | |
| 25 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--allpairs_global)" /> | |
| 26 <expand macro="id_and_iddef" /> | |
| 27 <param name="acceptall" type="boolean" truevalue="--acceptall" falsevalue="" checked="False" | |
| 28 label="Output all pairwise alignments" help="This option overrides all other accept/reject options including identity. (--acceptall)"/> | |
| 29 <param name="query_cov" type="float" value="" optional="True" label="Reject if fraction of query seq. aligned lower than this value" | |
| 30 help="(--query_cov)"/> | |
| 31 <expand macro="userfields" /> | |
| 32 </inputs> | |
| 33 <outputs> | |
| 34 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> | |
| 35 </outputs> | |
| 36 <tests> | |
| 37 <test> | |
| 38 <param name="infile" value="Rfam_11_0.repr.fasta.bz2" ftype="fasta" /> | |
| 39 <param name="acceptall" value=""/> | |
| 40 <param name="id" value="0.97"/> | |
| 41 <param name="query_cov" value="0.95"/> | |
| 42 <param name="userfields" value="query,target"/> | |
| 43 <output name="outfile" file="alignment_result1.fasta" lines_diff="4" ftype="fasta" /> | |
| 44 </test> | |
| 45 </tests> | |
| 46 <help> | |
| 47 <![CDATA[ | |
| 48 **What it does** | |
| 49 | |
| 50 Pairwise alignments of all sequences. | |
| 51 | |
| 52 | |
| 53 Alignment options (most searching options also apply) | |
| 54 --allpairs_global FILENAME perform global alignment of all sequence pairs | |
| 55 --alnout FILENAME filename for human-readable alignment output | |
| 56 --acceptall output all pairwise alignments | |
| 57 | |
| 58 @EXTERNAL_DOCUMENTATION@ | |
| 59 | |
| 60 | |
| 61 ]]> | |
| 62 </help> | |
| 63 <expand macro="citations" /> | |
| 64 </tool> |