Mercurial > repos > iuc > vsearch
comparison alignment.xml @ 0:fae6527990af draft
Imported from capsule None
| author | iuc |
|---|---|
| date | Thu, 21 May 2015 03:58:09 -0400 |
| parents | |
| children | f29e21388219 |
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| -1:000000000000 | 0:fae6527990af |
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| 1 <tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.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 | |
| 14 --id $id | |
| 15 --iddef $iddef | |
| 16 --allpairs_global "$infile" | |
| 17 --alnout $outfile | |
| 18 --query_cov $query_cov | |
| 19 @USERFIELDS@ | |
| 20 ]]> | |
| 21 </command> | |
| 22 <inputs> | |
| 23 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--allpairs_global)" /> | |
| 24 <expand macro="id_and_iddef" /> | |
| 25 <param name="acceptall" type="boolean" truevalue="--acceptall" falsevalue="" checked="False" | |
| 26 label="Output all pairwise alignments" help="This option overrides all other accept/reject options including identity. (--acceptall)"/> | |
| 27 <param name="query_cov" type="float" value="" optional="True" label="Reject if fraction of query seq. aligned lower than this value" | |
| 28 help="(--query_cov)"/> | |
| 29 <expand macro="userfields" /> | |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> | |
| 33 </outputs> | |
| 34 <tests> | |
| 35 <test> | |
| 36 <param name="infile" value="Rfam_11_0.repr.fasta.bz2" ftype="fasta" /> | |
| 37 <param name="acceptall" value=""/> | |
| 38 <param name="id" value="0.97"/> | |
| 39 <param name="query_cov" value="0.95"/> | |
| 40 <param name="userfields" value="query,target"/> | |
| 41 <output name="outfile" file="alignment_result1.fasta" lines_diff="4" ftype="fasta" /> | |
| 42 </test> | |
| 43 </tests> | |
| 44 <help> | |
| 45 <![CDATA[ | |
| 46 **What it does** | |
| 47 | |
| 48 Pairwise alignments of all sequences. | |
| 49 | |
| 50 | |
| 51 Alignment options (most searching options also apply) | |
| 52 --allpairs_global FILENAME perform global alignment of all sequence pairs | |
| 53 --alnout FILENAME filename for human-readable alignment output | |
| 54 --acceptall output all pairwise alignments | |
| 55 | |
| 56 @EXTERNAL_DOCUMENTATION@ | |
| 57 | |
| 58 ------- | |
| 59 | |
| 60 @REFERENCES@ | |
| 61 | |
| 62 | |
| 63 ]]> | |
| 64 </help> | |
| 65 <expand macro="citations" /> | |
| 66 </tool> |