Mercurial > repos > devteam > emboss_5
comparison emboss_twofeat.xml @ 10:d49956b87f7e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author | iuc |
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date | Wed, 08 Feb 2017 12:42:22 -0500 |
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children | 8992d258e42f |
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9:511429456d3c | 10:d49956b87f7e |
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1 <tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0.1"> | |
2 <description>Finds neighbouring pairs of features in sequences</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <code file="emboss_format_corrector.py" /> | |
8 <command>twofeat -sequence '$input1' -outfile '$out_file1' -atype '$atype' -btype '$btype' -minrange $minrange -maxrange $maxrange -asource '$asource' -asense $asense -aminscore $aminscore | |
9 -amaxscore $amaxscore -atag '$atag' -avalue '$avalue' -bsource '$bsource' -bsense $bsense -bminscore $bminscore -bmaxscore $bmaxscore -btag '$btag' -bvalue '$bvalue' -overlap $overlap | |
10 -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout '$typeout' -rformat2 $out_format1 -auto</command> | |
11 <inputs> | |
12 <param name="input1" type="data" format="data" label="Sequences" /> | |
13 <param name="atype" type="text" value="*" label="Feature type you wish to allow. Feature 1" /> | |
14 <param name="btype" type="text" value="*" label="Feature type you wish to allow. Feature 2" /> | |
15 <param name="minrange" type="integer" value="0" label="Minimun range" /> | |
16 <param name="maxrange" type="integer" value="0" label="Maximum range" /> | |
17 <param name="asource" type="text" value="*" label="Feature source 1" /> | |
18 <param name="asense" type="select" label="Feature sense 1"> | |
19 <option value="0">Any sense</option> | |
20 <option value="+">Forward sense</option> | |
21 <option value="-">Reverse sense</option> | |
22 </param> | |
23 <param name="aminscore" type="float" value="0.0" label="Feature 1 minimum score" /> | |
24 <param name="amaxscore" type="float" value="0.0" label="Feature1 maximum score" /> | |
25 <param name="atag" type="text" value="*" label="Feature 1 tags" /> | |
26 <param name="avalue" type="text" value="*" label="Feature 1 tag values" /> | |
27 <param name="bsource" type="text" value="*" label="Feature 2 source" /> | |
28 <param name="bsense" type="select" label="Feature 2 sense"> | |
29 <option value="0">Any sense</option> | |
30 <option value="+">Forward sense</option> | |
31 <option value="-">Reverse sense</option> | |
32 </param> | |
33 <param name="bminscore" type="float" value="0.0" label="Feature 2 minimum score" /> | |
34 <param name="bmaxscore" type="float" value="0.0" label="Feature 2 maximum score" /> | |
35 <param name="btag" type="text" value="*" label="Feature 2 tags" /> | |
36 <param name="bvalue" type="text" value="*" label="Feature 2 tag values" /> | |
37 <param name="overlap" type="select" label="Allowed overlaps"> | |
38 <option value="A">Any</option> | |
39 <option value="O">Overlap required but not within</option> | |
40 <option value="NO">No overlaps are allowed</option> | |
41 <option value="NW:">Overlap required but not within</option> | |
42 <option value="AW">A must be all within B</option> | |
43 <option value="BW">B must be all within A</option> | |
44 </param> | |
45 <param name="rangetype" type="select" label="How to determine range"> | |
46 <option value="N">From nearest ends</option> | |
47 <option value="L">From left ends</option> | |
48 <option value="R">From right ends</option> | |
49 <option value="F">From furthest ends</option> | |
50 </param> | |
51 <param name="sense" type="select" label="Required sense"> | |
52 <option value="A">Any sense</option> | |
53 <option value="S">Same sense</option> | |
54 <option value="O">Opposite sense</option> | |
55 </param> | |
56 <param name="order" type="select" label="Required order of the two features"> | |
57 <option value="A">Any</option> | |
58 <option value="AB">Feature A then feature B</option> | |
59 <option value="BA">Feature B then feature A</option> | |
60 </param> | |
61 <param name="twoout" type="select" label="Write out the two features themselves"> | |
62 <option value="no">No</option> | |
63 <option value="yes">Yes</option> | |
64 </param> | |
65 <param name="typeout" type="text" value="misc_feature" label="New feature type" /> | |
66 <param name="out_format1" type="select" label="Output report file format"> | |
67 <option value="table">Table</option> | |
68 <option value="embl">EMBL</option> | |
69 <option value="genbank">GENBANK</option> | |
70 <option value="gff">GFF</option> | |
71 <option value="pir">PIR</option> | |
72 <option value="swiss">SwissProt</option> | |
73 <option value="dbmotif">DbMotif</option> | |
74 <option value="diffseq">Diffseq</option> | |
75 <option value="excel">Excel (tab delimited)</option> | |
76 <option value="feattable">FeatTable</option> | |
77 <option value="motif">Motif</option> | |
78 <option value="regions">Regions</option> | |
79 <option value="seqtable">SeqTable</option> | |
80 <option value="simple">SRS Simple</option> | |
81 <option value="srs">SRS</option> | |
82 <option value="tagseq">TagSeq</option> | |
83 </param> | |
84 </inputs> | |
85 <outputs> | |
86 <data name="out_file1" format="table" /> | |
87 </outputs> | |
88 <help> | |
89 You can view the original documentation here_. | |
90 | |
91 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/twofeat.html | |
92 </help> | |
93 <expand macro="citations" /> | |
94 </tool> |