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comparison tools/emboss_5/emboss_msbar.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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>