root/galaxy-central/tools/emboss_5/emboss_msbar.xml @ 3

リビジョン 2, 4.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
109The 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>
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