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comparison alignment.xml @ 0:24e4f42410e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
author iuc
date Mon, 11 May 2015 22:46:54 -0400
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-1:000000000000 0:24e4f42410e5
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>