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comparison glang-galaxy-conf/kbws/kblast.xml @ 2:8947fca5f715 draft default tip

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author ktnyt
date Fri, 26 Jun 2015 05:21:44 -0400
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1:84a17b3fad1f 2:8947fca5f715
1 <tool id="EMBOSS: kblast" name="kblast" version="1.0.2">
2 <description>Search similar sequences in public repositories using BLAST</description>
3 <command>kblast -seqall $input1 -database $database -program $program -server $server -format $format -eval $eval -qfilter $qfilter -opengap $opengap -extendgap $extendgap -dropoff $dropoff -penalty $penalty -reward $reward -numdescriptions $numdescriptions -numalignments $numalignments -threshold $threshold -g $g -matrix $matrix -wordsize $wordsize -dbsize $dbsize -k $k -searchsp $searchsp -auto -outfile $out_file1</command>
4 <inputs>
5 <param format="data" name="input1" type="data">
6 <label>Sequence</label>
7 </param>
8 <param name="database" size="4" type="text" value="swissprot">
9 <label>database name about target for your search</label>
10 </param>
11 <param name="program" size="4" type="text" value="auto">
12 <label>blast program name. 'auto' (infer suitable program from your sequence), 'blastn', 'blastp' or 'blastx'</label>
13 </param>
14 <param name="server" size="4" type="text" value="">
15 <label>specify web server for your search. 'NCBI', 'EBI' or 'DDBJ'</label>
16 </param>
17 <param name="format" size="4" type="text" value="0">
18 <label>blast report format. 0 : normal BLAST report 8 : tabulark 1: ID listk 2: ID list separated by conmma</label>
19 </param>
20 <param name="eval" size="4" type="text" value="10.0">
21 <label>Expectation value</label>
22 </param>
23 <param name="qfilter" size="4" type="text" value="T">
24 <label></label>
25 </param>
26 <param name="opengap" size="4" type="integer" value="-1">
27 <label>cost to open a gap</label>
28 </param>
29 <param name="extendgap" size="4" type="integer" value="-1">
30 <label>cost to extend a gap</label>
31 </param>
32 <param name="dropoff" size="4" type="text" value="0">
33 <label>X dropoff value for gapped alignment (in bits)</label>
34 </param>
35 <param name="penalty" size="4" type="integer" value="-3">
36 <label>penalty for a nucleotide mismatch (blastn only)</label>
37 </param>
38 <param name="reward" size="4" type="integer" value="1">
39 <label>reward for a nucleotide match (blastn only)</label>
40 </param>
41 <param name="numdescriptions" size="4" type="integer" value="500">
42 <label>show one-line descriptions for this number of database sequences</label>
43 </param>
44 <param name="numalignments" size="4" type="integer" value="250">
45 <label>number of database sequence to show alignments for (B)</label>
46 </param>
47 <param name="threshold" size="4" type="integer" value="0">
48 <label>threshold for extending hits, default if zero for each program</label>
49 </param>
50 <param name="g" type="select" value="no">
51 <label>perform gapped alignment</label>
52 <option value="no">No</option>
53 <option value="yes">Yes</option>
54 </param>
55 <param name="matrix" size="4" type="text" value="BLOSUM62">
56 <label>matrix</label>
57 </param>
58 <param name="wordsize" size="4" type="integer" value="0">
59 <label>word size, default if zero for each program</label>
60 </param>
61 <param name="dbsize" size="4" type="float" value="0">
62 <label>effective size of the database</label>
63 </param>
64 <param name="k" size="4" type="integer" value="0">
65 <label>number of best hits from a region to keep</label>
66 </param>
67 <param name="searchsp" size="4" type="float" value="0">
68 <label>effective length of the search space</label>
69 </param>
70
71 </inputs>
72 <outputs>
73 <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
74 </outputs>
75 </tool>