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comparison emboss_twofeat.xml @ 10:9b98d3d903c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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9:18a63c800a4d 10:9b98d3d903c6
1 <tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0">
2 <description>Finds neighbouring pairs of features in sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>twofeat -sequence $input1 -outfile $out_file1 -atype "$atype" -btype "$btype" -minrange "$minrange" -maxrange "$maxrange" -asource "$asource" -asense $asense -aminscore "$aminscore"
5 -amaxscore "$amaxscore" -atag "$atag" -avalue "$avalue" -bsource "$bsource" -bsense "$bsense" -bminscore "$bminscore" -bmaxscore "$bmaxscore" -btag "$btag" -bvalue "$bvalue" -overlap $overlap
6 -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout "$typeout" -rformat2 $out_format1 -auto</command>
7 <inputs>
8 <param format="data" name="input1" type="data">
9 <label>Sequences</label>
10 </param>
11 <param name="atype" type="text" value="*">
12 <label>Feature type you wish to allow. Feature 1</label>
13 </param>
14 <param name="btype" type="text" value="*">
15 <label>Feature type you wish to allow. Feature 2</label>
16 </param>
17 <param name="minrange" type="text" value="0">
18 <label>Minimun range</label>
19 </param>
20 <param name="maxrange" type="text" value="0">
21 <label>Maximum range</label>
22 </param>
23 <param name="asource" type="text" value="*">
24 <label>Feature source 1</label>
25 </param>
26 <param name="asense" type="select">
27 <label>Feature sense 1</label>
28 <option value="0">Any sense</option>
29 <option value="+">Forward sense</option>
30 <option value="-">Reverse sense</option>
31 </param>
32 <param name="aminscore" type="text" value="0.0">
33 <label>Feature 1 minimum score</label>
34 </param>
35 <param name="amaxscore" type="text" value="0.0">
36 <label>Feature1 maxiumum score</label>
37 </param>
38 <param name="atag" type="text" value="*">
39 <label>Feature 1 tag</label>
40 </param>
41 <param name="avalue" type="text" value="*">
42 <label>Tag 1 value</label>
43 </param>
44 <param name="bsource" type="text" value="*">
45 <label>Feature 2 source</label>
46 </param>
47 <param name="bsense" type="select">
48 <label>Feature 2 sense</label>
49 <option value="0">Any sense</option>
50 <option value="+">Forward sense</option>
51 <option value="-">Reverse sense</option>
52 </param>
53 <param name="bminscore" type="text" value="0.0">
54 <label>Feature 2 miniumum score</label>
55 </param>
56 <param name="bmaxscore" type="text" value="0.0">
57 <label>Feature 2 maximum score</label>
58 </param>
59 <param name="btag" type="text" value="*">
60 <label>Feature 2 tag</label>
61 </param>
62 <param name="bvalue" type="text" value="*">
63 <label>Feature 2 tag value</label>
64 </param>
65 <param name="overlap" type="select">
66 <label>opverlaps allowed</label>
67 <option value="A">Any</option>
68 <option value="O">Overlap required but not within</option>
69 <option value="NO">No overlaps are allowed</option>
70 <option value="NW:">Overlap required but not within</option>
71 <option value="AW">A must be all within B</option>
72 <option value="BW">B must be all within A</option>
73 </param>
74 <param name="rangetype" type="select">
75 <label>How to determine range</label>
76 <option value="N">From nearest ends</option>
77 <option value="L">From left ends</option>
78 <option value="R">From right ends</option>
79 <option value="F">From furthest ends</option>
80 </param>
81 <param name="sense" type="select">
82 <label>Required sense</label>
83 <option value="A">Any sense</option>
84 <option value="S">Same sense</option>
85 <option value="O">Opposite sense</option>
86 </param>
87 <param name="order" type="select">
88 <label>Required order of the two features</label>
89 <option value="A">Any</option>
90 <option value="AB">Feature A then feature B</option>
91 <option value="BA">Feature B then feature A</option>
92 </param>
93 <param name="twoout" type="select">
94 <label>Write out the two features themselves</label>
95 <option value="no">No</option>
96 <option value="yes">Yes</option>
97 </param>
98 <param name="typeout" type="text" value="misc_feature">
99 <label>New feature type</label>
100 </param>
101 <param name="out_format1" type="select">
102 <label>Output Report File Format</label>
103 <option value="table">Table</option>
104 <option value="embl">EMBL</option>
105 <option value="genbank">GENBANK</option>
106 <option value="gff">GFF</option>
107 <option value="pir">PIR</option>
108 <option value="swiss">SwissProt</option>
109 <option value="dbmotif">DbMotif</option>
110 <option value="diffseq">Diffseq</option>
111 <option value="excel">Excel (tab delimited)</option>
112 <option value="feattable">FeatTable</option>
113 <option value="motif">Motif</option>
114 <option value="regions">Regions</option>
115 <option value="seqtable">SeqTable</option>
116 <option value="simple">SRS Simple</option>
117 <option value="srs">SRS</option>
118 <option value="tagseq">TagSeq</option>
119 </param>
120 </inputs>
121 <outputs>
122 <data format="table" name="out_file1" />
123 </outputs>
124 <code file="emboss_format_corrector.py" />
125 <help>
126 You can view the original documentation here_.
127
128 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/twofeat.html
129
130 ------
131
132 **Citation**
133
134 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
135
136 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
137 </help>
138 </tool>