|
0
|
1 <tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0">
|
|
|
2 <description>Align EST and genomic DNA sequences</description>
|
|
|
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
|
|
4 <command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
|
|
|
5 $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command>
|
|
|
6 <inputs>
|
|
|
7 <param format="fasta" name="input1" type="data">
|
|
|
8 <label>EST sequence(s)</label>
|
|
|
9 </param>
|
|
|
10 <param format="data" name="input2" type="data">
|
|
|
11 <label>Genomic sequence</label>
|
|
|
12 </param>
|
|
|
13 <param name="match" size="4" type="text" value="1">
|
|
|
14 <label>Score for matching two bases</label>
|
|
|
15 </param>
|
|
|
16 <param name="mismatch" size="4" type="text" value="1">
|
|
|
17 <label>Cost for mismatching two bases</label>
|
|
|
18 </param>
|
|
|
19 <param name="gappenalty" size="4" type="text" value="2">
|
|
|
20 <label>Cost for deleting a single base in either sequence, excluding introns</label>
|
|
|
21 </param>
|
|
|
22 <param name="intronpenalty" size="4" type="text" value="40">
|
|
|
23 <label>Cost for an intron, independent of length</label>
|
|
|
24 </param>
|
|
|
25 <param name="splicepenalty" size="4" type="text" value="20">
|
|
|
26 <label>Cost for an intron, independent of length and starting/ending on donor-acceptor sites</label>
|
|
|
27 </param>
|
|
|
28 <param name="minscore" size="4" type="text" value="30">
|
|
|
29 <label>Exclude alignments with scores below this threshold score</label>
|
|
|
30 </param>
|
|
|
31 <param name="reverse" type="select">
|
|
|
32 <label>Reverse the orientation of the EST sequence</label>
|
|
|
33 <option value="no">No</option>
|
|
|
34 <option value="yes">Yes</option>
|
|
|
35 </param>
|
|
|
36 <param name="splice" type="select">
|
|
|
37 <label>Use donor and acceptor splice sites</label>
|
|
|
38 <option value="yes">Yes</option>
|
|
|
39 <option value="no">No</option>
|
|
|
40 </param>
|
|
|
41 <param name="mode" type="select">
|
|
|
42 <label>Comparison mode</label>
|
|
|
43 <option value="both">Both strands</option>
|
|
|
44 <option value="forward">Forward strand only</option>
|
|
|
45 <option value="reverse">Reverse strand only</option>
|
|
|
46 </param>
|
|
|
47 <param name="best" type="select">
|
|
|
48 <label>Only best comparisons</label>
|
|
|
49 <option value="yes">Yes</option>
|
|
|
50 <option value="no">No</option>
|
|
|
51 </param>
|
|
|
52 <param name="shuffle" size="4" type="text" value="0">
|
|
|
53 <label>Shuffle</label>
|
|
|
54 </param>
|
|
|
55 <param name="seed" size="4" type="text" value="20825">
|
|
|
56 <label>Random number seed</label>
|
|
|
57 </param>
|
|
|
58 <param name="align" type="select">
|
|
|
59 <label>Show the alignment</label>
|
|
|
60 <option value="no">No</option>
|
|
|
61 <option value="yes">Yes</option>
|
|
|
62 </param>
|
|
|
63 <param name="width" size="4" type="text" value="50">
|
|
|
64 <label>Alignment width</label>
|
|
|
65 </param>
|
|
|
66 </inputs>
|
|
|
67 <outputs>
|
|
|
68 <data format="est2genome" name="out_file1" />
|
|
|
69 </outputs>
|
|
|
70 <tests>
|
|
|
71 <test>
|
|
|
72 <param name="input1" value="2.fasta"/>
|
|
|
73 <param name="input2" value="1.fasta"/>
|
|
|
74 <param name="match" value="1"/>
|
|
|
75 <param name="mismatch" value="1"/>
|
|
|
76 <param name="match" value="1"/>
|
|
|
77 <param name="gappenalty" value="2"/>
|
|
|
78 <param name="intronpenalty" value="40"/>
|
|
|
79 <param name="splicepenalty" value="20"/>
|
|
|
80 <param name="minscore" value="30"/>
|
|
|
81 <param name="reverse" value="no"/>
|
|
|
82 <param name="splice" value="yes"/>
|
|
|
83 <param name="mode" value="both"/>
|
|
|
84 <param name="best" value="yes"/>
|
|
|
85 <param name="shuffle" value="0"/>
|
|
|
86 <param name="seed" value="20825"/>
|
|
|
87 <param name="align" value="no"/>
|
|
|
88 <param name="width" value="50"/>
|
|
|
89 <output name="out_file1" file="emboss_est2genome_out.est2genome"/>
|
|
|
90 </test>
|
|
|
91 </tests>
|
|
|
92 <help>
|
|
|
93 .. class:: warningmark
|
|
|
94
|
|
|
95 The input dataset needs to be sequences.
|
|
|
96
|
|
|
97 -----
|
|
|
98
|
|
|
99 You can view the original documentation here_.
|
|
|
100
|
|
|
101 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.html
|
|
|
102 </help>
|
|
|
103 </tool>
|
