|
2
|
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>
|
