Mercurial > repos > ktnyt > gembassy
comparison glang-galaxy-conf/kbws/kssearch.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: kssearch" name="kssearch" version="1.0.2"> | |
2 <description>Search similar sequences in public repositories using SSEARCH</description> | |
3 <command>kssearch -seqall $input1 -moltype $moltype -histogram $histogram -nucleotide $nucleotide -topstrand $topstrand -bottomstrand $bottomstrand -gapopen $gapopen -gapext $gapext -scores $scores -alignments $alignments -ktup $ktup -matrix $matrix -eupper $eupper -elower $elower -dbrange $dbrange -seqrange $seqrange -auto -outfile $out_file1</command> | |
4 <inputs> | |
5 <param format="data" name="input1" type="data"> | |
6 <label>Sequence</label> | |
7 </param> | |
8 <param name="moltype" size="4" type="text" value=""> | |
9 <label>molecular type</label> | |
10 </param> | |
11 <param name="histogram" type="select" value=""> | |
12 <label>Display histogram</label> | |
13 <option value="no">No</option> | |
14 <option value="yes">Yes</option> | |
15 </param> | |
16 <param name="nucleotide" type="select" value=""> | |
17 <label>your query is nucleotide or not(protein)</label> | |
18 <option value="no">No</option> | |
19 <option value="yes">Yes</option> | |
20 </param> | |
21 <param name="topstrand" type="select" value=""> | |
22 <label>Nucleotide sequence strand to use for seqrch (top)</label> | |
23 <option value="no">No</option> | |
24 <option value="yes">Yes</option> | |
25 </param> | |
26 <param name="bottomstrand" type="select" value=""> | |
27 <label>Nucleotide sequence strand to use for seqrch (bottom)</label> | |
28 <option value="no">No</option> | |
29 <option value="yes">Yes</option> | |
30 </param> | |
31 <param name="gapopen" size="4" type="integer" value=""> | |
32 <label>Score for the initiation of a gap</label> | |
33 </param> | |
34 <param name="gapext" size="4" type="integer" value=""> | |
35 <label>Score for each base/residue in a gap</label> | |
36 </param> | |
37 <param name="scores" size="4" type="integer" value=""> | |
38 <label>Maximum number of scores displayed in the output</label> | |
39 </param> | |
40 <param name="alignments" size="4" type="integer" value=""> | |
41 <label>Maximum number of alignments displayed in the output</label> | |
42 </param> | |
43 <param name="ktup" size="4" type="integer" value=""> | |
44 <label>Word size to use for sequence comparisons</label> | |
45 </param> | |
46 <param name="matrix" size="4" type="text" value=""> | |
47 <label>Scoring matrix to be used in the search</label> | |
48 </param> | |
49 <param name="eupper" size="4" type="float" value=""> | |
50 <label>Upper E-value threshold</label> | |
51 </param> | |
52 <param name="elower" size="4" type="float" value=""> | |
53 <label>Lower E-value threshold</label> | |
54 </param> | |
55 <param name="dbrange" size="4" type="text" value=""> | |
56 <label>Range of sequence lengths in search database to include in search</label> | |
57 </param> | |
58 <param name="seqrange" size="4" type="text" value=""> | |
59 <label>Region of the query sequence to use for the search</label> | |
60 </param> | |
61 | |
62 </inputs> | |
63 <outputs> | |
64 <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" /> | |
65 </outputs> | |
66 </tool> |