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comparison emboss_twofeat.xml @ 11:0e2484b6829b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
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10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0"> 1 <tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0.1">
2 <description>Finds neighbouring pairs of features in sequences</description> 2 <description>Finds neighbouring pairs of features in sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>twofeat -sequence $input1 -outfile $out_file1 -atype "$atype" -btype "$btype" -minrange "$minrange" -maxrange "$maxrange" -asource "$asource" -asense $asense -aminscore "$aminscore" 4 <import>macros.xml</import>
5 -amaxscore "$amaxscore" -atag "$atag" -avalue "$avalue" -bsource "$bsource" -bsense "$bsense" -bminscore "$bminscore" -bmaxscore "$bmaxscore" -btag "$btag" -bvalue "$bvalue" -overlap $overlap 5 </macros>
6 -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout "$typeout" -rformat2 $out_format1 -auto</command> 6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>twofeat -sequence '$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>
7 <inputs> 11 <inputs>
8 <param format="data" name="input1" type="data"> 12 <param name="input1" type="data" format="data" label="Sequences" />
9 <label>Sequences</label> 13 <param name="atype" type="text" value="*" label="Feature type you wish to allow. Feature 1" />
10 </param> 14 <param name="btype" type="text" value="*" label="Feature type you wish to allow. Feature 2" />
11 <param name="atype" type="text" value="*"> 15 <param name="minrange" type="integer" value="0" label="Minimun range" />
12 <label>Feature type you wish to allow. Feature 1</label> 16 <param name="maxrange" type="integer" value="0" label="Maximum range" />
13 </param> 17 <param name="asource" type="text" value="*" label="Feature source 1" />
14 <param name="btype" type="text" value="*"> 18 <param name="asense" type="select" label="Feature sense 1">
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> 19 <option value="0">Any sense</option>
29 <option value="+">Forward sense</option> 20 <option value="+">Forward sense</option>
30 <option value="-">Reverse sense</option> 21 <option value="-">Reverse sense</option>
31 </param> 22 </param>
32 <param name="aminscore" type="text" value="0.0"> 23 <param name="aminscore" type="float" value="0.0" label="Feature 1 minimum score" />
33 <label>Feature 1 minimum score</label> 24 <param name="amaxscore" type="float" value="0.0" label="Feature1 maximum score" />
34 </param> 25 <param name="atag" type="text" value="*" label="Feature 1 tags" />
35 <param name="amaxscore" type="text" value="0.0"> 26 <param name="avalue" type="text" value="*" label="Feature 1 tag values" />
36 <label>Feature1 maxiumum score</label> 27 <param name="bsource" type="text" value="*" label="Feature 2 source" />
37 </param> 28 <param name="bsense" type="select" label="Feature 2 sense">
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> 29 <option value="0">Any sense</option>
50 <option value="+">Forward sense</option> 30 <option value="+">Forward sense</option>
51 <option value="-">Reverse sense</option> 31 <option value="-">Reverse sense</option>
52 </param> 32 </param>
53 <param name="bminscore" type="text" value="0.0"> 33 <param name="bminscore" type="float" value="0.0" label="Feature 2 minimum score" />
54 <label>Feature 2 miniumum score</label> 34 <param name="bmaxscore" type="float" value="0.0" label="Feature 2 maximum score" />
55 </param> 35 <param name="btag" type="text" value="*" label="Feature 2 tags" />
56 <param name="bmaxscore" type="text" value="0.0"> 36 <param name="bvalue" type="text" value="*" label="Feature 2 tag values" />
57 <label>Feature 2 maximum score</label> 37 <param name="overlap" type="select" label="Allowed overlaps">
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> 38 <option value="A">Any</option>
68 <option value="O">Overlap required but not within</option> 39 <option value="O">Overlap required but not within</option>
69 <option value="NO">No overlaps are allowed</option> 40 <option value="NO">No overlaps are allowed</option>
70 <option value="NW:">Overlap required but not within</option> 41 <option value="NW:">Overlap required but not within</option>
71 <option value="AW">A must be all within B</option> 42 <option value="AW">A must be all within B</option>
72 <option value="BW">B must be all within A</option> 43 <option value="BW">B must be all within A</option>
73 </param> 44 </param>
74 <param name="rangetype" type="select"> 45 <param name="rangetype" type="select" label="How to determine range">
75 <label>How to determine range</label>
76 <option value="N">From nearest ends</option> 46 <option value="N">From nearest ends</option>
77 <option value="L">From left ends</option> 47 <option value="L">From left ends</option>
78 <option value="R">From right ends</option> 48 <option value="R">From right ends</option>
79 <option value="F">From furthest ends</option> 49 <option value="F">From furthest ends</option>
80 </param> 50 </param>
81 <param name="sense" type="select"> 51 <param name="sense" type="select" label="Required sense">
82 <label>Required sense</label>
83 <option value="A">Any sense</option> 52 <option value="A">Any sense</option>
84 <option value="S">Same sense</option> 53 <option value="S">Same sense</option>
85 <option value="O">Opposite sense</option> 54 <option value="O">Opposite sense</option>
86 </param> 55 </param>
87 <param name="order" type="select"> 56 <param name="order" type="select" label="Required order of the two features">
88 <label>Required order of the two features</label>
89 <option value="A">Any</option> 57 <option value="A">Any</option>
90 <option value="AB">Feature A then feature B</option> 58 <option value="AB">Feature A then feature B</option>
91 <option value="BA">Feature B then feature A</option> 59 <option value="BA">Feature B then feature A</option>
92 </param> 60 </param>
93 <param name="twoout" type="select"> 61 <param name="twoout" type="select" label="Write out the two features themselves">
94 <label>Write out the two features themselves</label>
95 <option value="no">No</option> 62 <option value="no">No</option>
96 <option value="yes">Yes</option> 63 <option value="yes">Yes</option>
97 </param> 64 </param>
98 <param name="typeout" type="text" value="misc_feature"> 65 <param name="typeout" type="text" value="misc_feature" label="New feature type" />
99 <label>New feature type</label> 66 <param name="out_format1" type="select" label="Output report file format">
100 </param>
101 <param name="out_format1" type="select">
102 <label>Output Report File Format</label>
103 <option value="table">Table</option> 67 <option value="table">Table</option>
104 <option value="embl">EMBL</option> 68 <option value="embl">EMBL</option>
105 <option value="genbank">GENBANK</option> 69 <option value="genbank">GENBANK</option>
106 <option value="gff">GFF</option> 70 <option value="gff">GFF</option>
107 <option value="pir">PIR</option> 71 <option value="pir">PIR</option>
117 <option value="srs">SRS</option> 81 <option value="srs">SRS</option>
118 <option value="tagseq">TagSeq</option> 82 <option value="tagseq">TagSeq</option>
119 </param> 83 </param>
120 </inputs> 84 </inputs>
121 <outputs> 85 <outputs>
122 <data format="table" name="out_file1" /> 86 <data name="out_file1" format="table" />
123 </outputs> 87 </outputs>
124 <code file="emboss_format_corrector.py" />
125 <help> 88 <help>
126 You can view the original documentation here_. 89 You can view the original documentation here_.
127
128 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/twofeat.html
129 90
130 ------ 91 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/twofeat.html
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> 92 </help>
93 <expand macro="citations" />
138 </tool> 94 </tool>