Mercurial > repos > devteam > emboss_5

comparison emboss_twofeat.xml @ 10:d49956b87f7e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
parents
children 8992d258e42f
comparison
equal deleted inserted replaced
9:511429456d3c 10:d49956b87f7e
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>