|
0
|
1 <tool id="EMBOSS: msbar55" name="msbar" version="5.0.0">
|
|
|
2 <description>Mutate sequence beyond all recognition</description>
|
|
|
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
|
|
4 <command>msbar -sequence $input1 -outseq $out_file1 -count $count -point $point -block $block -codon $codon -inframe $inframe -minimum $minimum -maximum $maximum -osformat2 $out_format1
|
|
|
5 -auto</command>
|
|
|
6 <inputs>
|
|
|
7 <param format="fasta" name="input1" type="data">
|
|
|
8 <label>Sequence 1</label>
|
|
|
9 </param>
|
|
|
10 <param name="count" size="4" type="text" value="1">
|
|
|
11 <label>Number of times to perform the mutation operations</label>
|
|
|
12 </param>
|
|
|
13 <param name="point" type="select">
|
|
|
14 <label>Types of point mutations to perform</label>
|
|
|
15 <option value="0">None</option>
|
|
|
16 <option value="1">Any of the following</option>
|
|
|
17 <option value="2">Insertions</option>
|
|
|
18 <option value="3">Deletions</option>
|
|
|
19 <option value="4">Changes</option>
|
|
|
20 <option value="5">Duplications</option>
|
|
|
21 <option value="6">Moves</option>
|
|
|
22 </param>
|
|
|
23 <param name="block" type="select">
|
|
|
24 <label>Types of block mutations to perform</label>
|
|
|
25 <option value="0">None</option>
|
|
|
26 <option value="1">Any of the following</option>
|
|
|
27 <option value="2">Insertions</option>
|
|
|
28 <option value="3">Deletions</option>
|
|
|
29 <option value="4">Changes</option>
|
|
|
30 <option value="5">Duplications</option>
|
|
|
31 <option value="6">Moves</option>
|
|
|
32 </param>
|
|
|
33 <param name="codon" type="select">
|
|
|
34 <label>Types of codon mutations to perform. These are only done if the sequence is nucleic</label>
|
|
|
35 <option value="0">None</option>
|
|
|
36 <option value="1">Any of the following</option>
|
|
|
37 <option value="2">Insertions</option>
|
|
|
38 <option value="3">Deletions</option>
|
|
|
39 <option value="4">Changes</option>
|
|
|
40 <option value="5">Duplications</option>
|
|
|
41 <option value="6">Moves</option>
|
|
|
42 </param>
|
|
|
43 <param name="inframe" type="select">
|
|
|
44 <label>Do 'codon' and 'block' operations in frame</label>
|
|
|
45 <option value="no">No</option>
|
|
|
46 <option value="yes">Yes</option>
|
|
|
47 </param>
|
|
|
48 <param name="minimum" size="4" type="text" value="1">
|
|
|
49 <label>Minimum size for a block mutation</label>
|
|
|
50 </param>
|
|
|
51 <param name="maximum" size="4" type="text" value="10">
|
|
|
52 <label>Maximum size for a block mutation</label>
|
|
|
53 </param>
|
|
|
54 <param name="out_format1" type="select">
|
|
|
55 <label>Output Sequence File Format</label>
|
|
|
56 <option value="fasta">FASTA (m)</option>
|
|
|
57 <option value="acedb">ACeDB (m)</option>
|
|
|
58 <option value="asn1">ASN.1 (m)</option>
|
|
|
59 <option value="clustal">Clustal (m)</option>
|
|
|
60 <option value="codata">CODATA (m)</option>
|
|
|
61 <option value="embl">EMBL (m)</option>
|
|
|
62 <option value="fitch">Fitch (m)</option>
|
|
|
63 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
|
|
|
64 <option value="genbank">GENBANK (m)</option>
|
|
|
65 <option value="gff">GFF (m)</option>
|
|
|
66 <option value="hennig86">Hennig86 (m)</option>
|
|
|
67 <option value="ig">Intelligenetics (m)</option>
|
|
|
68 <option value="jackknifer">Jackknifer (m)</option>
|
|
|
69 <option value="jackknifernon">Jackknifernon (m)</option>
|
|
|
70 <option value="mega">Mega (m)</option>
|
|
|
71 <option value="meganon">Meganon (m)</option>
|
|
|
72 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
|
|
|
73 <option value="pir">NBRF (PIR) (m)</option>
|
|
|
74 <option value="ncbi">NCBI style FASTA (m)</option>
|
|
|
75 <option value="nexus">Nexus/PAUP (m)</option>
|
|
|
76 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
|
|
|
77 <option value="phylip">PHYLIP interleaved (m)</option>
|
|
|
78 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
|
|
|
79 <option value="selex">SELEX (m)</option>
|
|
|
80 <option value="staden">Staden (s)</option>
|
|
|
81 <option value="strider">DNA strider (m)</option>
|
|
|
82 <option value="swiss">SwisProt entry (m)</option>
|
|
|
83 <option value="text">Plain sequence (s)</option>
|
|
|
84 <option value="treecon">Treecon (m)</option>
|
|
|
85 </param>
|
|
|
86 </inputs>
|
|
|
87 <outputs>
|
|
|
88 <data format="fasta" name="out_file1" />
|
|
|
89 </outputs>
|
|
|
90 <tests>
|
|
|
91 <test>
|
|
|
92 <param name="input1" value="2.fasta"/>
|
|
|
93 <param name="count" value="1"/>
|
|
|
94 <param name="point" value="0"/>
|
|
|
95 <param name="block" value="0"/>
|
|
|
96 <param name="codon" value="0"/>
|
|
|
97 <param name="inframe" value="no"/>
|
|
|
98 <param name="minimum" value="1"/>
|
|
|
99 <param name="maximum" value="10"/>
|
|
|
100 <param name="out_format1" value="fasta"/>
|
|
|
101 <output name="out_file1" file="emboss_msbar_out.fasta"/>
|
|
|
102 </test>
|
|
|
103 </tests>
|
|
|
104 <code file="emboss_format_corrector.py" />
|
|
|
105 <help>
|
|
|
106
|
|
|
107 .. class:: warningmark
|
|
|
108
|
|
|
109 The input dataset needs to be sequences.
|
|
|
110
|
|
|
111 -----
|
|
|
112
|
|
|
113 You can view the original documentation here_.
|
|
|
114
|
|
|
115 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/msbar.html
|
|
|
116 </help>
|
|
|
117 </tool>
|
