Mercurial > repos > ktnyt > gembassy
comparison glang-galaxy-conf/kbws/ktrnascan_se.xml @ 2:8947fca5f715 draft default tip
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author | ktnyt |
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date | Fri, 26 Jun 2015 05:21:44 -0400 |
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1:84a17b3fad1f | 2:8947fca5f715 |
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1 <tool id="EMBOSS: ktrnascan_se" name="ktrnascan_se" version="1.0.2"> | |
2 <description>Finds tRNA genes using tRNAscan-SE</description> | |
3 <command>ktrnascan_se -seqall $input1 -title $title -mode $mode -source $source -gcode $gcode -pesudogene $pesudogene -origin $origin -ace $ace -codons $codons -fpos $fpos -breakdown $breakdown -covescore $covescore -euparams $euparams -euscore $euscore -auto -outfile $out_file1</command> | |
4 <inputs> | |
5 <param format="data" name="input1" type="data"> | |
6 <label>Sequence</label> | |
7 </param> | |
8 <param name="title" size="4" type="text" value=""> | |
9 <label>Title of your job</label> | |
10 </param> | |
11 <param name="mode" size="4" type="text" value="Default"> | |
12 <label>Search mode</label> | |
13 </param> | |
14 <param name="source" size="4" type="text" value="Mixed (general tRNA model)"> | |
15 <label>Training data set</label> | |
16 </param> | |
17 <param name="gcode" size="4" type="text" value="Universal"> | |
18 <label>Genetic Code for tRNA Isotype Prediction</label> | |
19 </param> | |
20 <param name="pesudogene" type="select" value=""> | |
21 <label>Disable pseudo gene checking</label> | |
22 <option value="no">No</option> | |
23 <option value="yes">Yes</option> | |
24 </param> | |
25 <param name="origin" type="select" value=""> | |
26 <label>Show origin of first-pass hits</label> | |
27 <option value="no">No</option> | |
28 <option value="yes">Yes</option> | |
29 </param> | |
30 <param name="ace" type="select" value=""> | |
31 <label>Display results in ACeDB format</label> | |
32 <option value="no">No</option> | |
33 <option value="yes">Yes</option> | |
34 </param> | |
35 <param name="codons" type="select" value=""> | |
36 <label>Show codons instead of tRNA anticodons</label> | |
37 <option value="no">No</option> | |
38 <option value="yes">Yes</option> | |
39 </param> | |
40 <param name="fpos" type="select" value=""> | |
41 <label>Show false positives from tRNAscan/EufindtRNA</label> | |
42 <option value="no">No</option> | |
43 <option value="yes">Yes</option> | |
44 </param> | |
45 <param name="breakdown" type="select" value=""> | |
46 <label>Show primary and secondary structure components to Cove scores</label> | |
47 <option value="no">No</option> | |
48 <option value="yes">Yes</option> | |
49 </param> | |
50 <param name="covescore" size="4" type="text" value=""> | |
51 <label>Cove score cutoff</label> | |
52 </param> | |
53 <param name="euparams" size="4" type="text" value="Default"> | |
54 <label>EufindtRNA search parameters</label> | |
55 </param> | |
56 <param name="euscore" size="4" type="text" value=""> | |
57 <label>Intermediate score cutoff</label> | |
58 </param> | |
59 | |
60 </inputs> | |
61 <outputs> | |
62 <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" /> | |
63 </outputs> | |
64 </tool> |