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

リビジョン 2, 5.4 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: transeq101" name="transeq" version="5.0.0">
2  <description>Translate nucleic acid sequences</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>transeq -sequence $input1 -outseq $out_file1 -frame $frame -table $table -regions "$regions" -trim $trim -clean $clean -alternative $alternative -osformat2 $out_format1 -auto</command>
5  <inputs>
6    <param format="fasta" name="input1" type="data">
7      <label>Sequences</label>
8    </param>
9    <param name="frame" type="select">
10      <label>Frame(s) to translate</label>
11      <option value="1">Frame 1</option>
12      <option value="2">Frame 2</option>
13      <option value="3">Frame 3</option>
14      <option value="F">Forward three frames</option>
15      <option value="-1">Frame -1</option>
16      <option value="-2">Frame -2</option>
17      <option value="-3">Frame -3</option>
18      <option value="R">Reverse three frames</option>
19      <option value="6">All six frames</option>
20    </param>
21    <param name="table" type="select">
22      <label>Code to use</label>
23      <option value="0">Standard</option>
24      <option value="1">Standard (with alternative initiation codons)</option>
25      <option value="2">Vertebrate Mitochondrial</option>
26      <option value="3">Yeast Mitochondrial</option>
27      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
28      <option value="5">Invertebrate Mitochondrial</option>
29      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
30      <option value="9">Echinoderm Mitochondrial</option>
31      <option value="10">Euplotid Nuclear</option>
32      <option value="11">Bacterial</option>
33      <option value="12">Alternative Yeast Nuclear</option>
34      <option value="13">Ascidian Mitochondrial</option>
35      <option value="14">Flatworm Mitochondrial</option>
36      <option value="15">Blepharisma Macronuclear</option>
37      <option value="16">Chlorophycean Mitochondrial</option>
38      <option value="21">Trematode Mitochondrial</option>
39      <option value="22">Scenedesmus obliquus</option>
40      <option value="23">Thraustochytrium Mitochondrial</option>
41    </param>
42    <param name="regions" size="10" type="text" value="">
43      <label>Regions to translate</label>
44    </param>
45    <param name="trim" type="select">
46      <label>Remove all 'X' and '*' characters from the right end of the translation</label>
47      <option value="no">No</option>
48      <option value="yes">Yes</option>
49    </param>
50    <param name="clean" type="select">
51      <label>Change all STOP codon positions from the '*' character to 'X'</label>
52      <option value="no">No</option>
53      <option value="yes">Yes</option>
54    </param>
55    <param name="alternative" type="select">
56      <label>Define frame '-1' as using the set of codons starting with the last codon of the sequence</label>
57      <option value="no">No</option>
58      <option value="yes">Yes</option>
59    </param>
60    <param name="out_format1" type="select">
61      <label>Output Sequence File Format</label>
62      <option value="fasta">FASTA (m)</option>
63      <option value="acedb">ACeDB (m)</option>
64      <option value="asn1">ASN.1 (m)</option>
65      <option value="clustal">Clustal (m)</option>
66      <option value="codata">CODATA (m)</option>
67      <option value="embl">EMBL (m)</option>
68      <option value="fitch">Fitch (m)</option>
69      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
70      <option value="genbank">GENBANK (m)</option>
71      <option value="gff">GFF (m)</option>
72      <option value="hennig86">Hennig86 (m)</option>
73      <option value="ig">Intelligenetics (m)</option>
74      <option value="jackknifer">Jackknifer (m)</option>
75      <option value="jackknifernon">Jackknifernon (m)</option>
76      <option value="mega">Mega (m)</option>
77      <option value="meganon">Meganon (m)</option>
78      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
79      <option value="pir">NBRF (PIR) (m)</option>
80      <option value="ncbi">NCBI style FASTA (m)</option>
81      <option value="nexus">Nexus/PAUP (m)</option>
82      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
83      <option value="phylip">PHYLIP interleaved (m)</option>
84      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
85      <option value="selex">SELEX (m)</option>
86      <option value="staden">Staden (s)</option>
87      <option value="strider">DNA strider (m)</option>
88      <option value="swiss">SwisProt entry (m)</option>
89      <option value="text">Plain sequence (s)</option>
90      <option value="treecon">Treecon (m)</option>
91    </param>
92  </inputs>
93  <outputs>
94    <data format="fasta" name="out_file1" />
95  </outputs>
96  <tests>
97    <test>
98      <param name="input1" value="2.fasta"/>
99      <param name="frame" value="1"/>
100      <param name="table" value="0"/>
101      <param name="regions" value=""/>
102      <param name="trim" value="no"/>
103      <param name="clean" value="no"/>
104      <param name="alternative" value="no"/>
105      <param name="out_format1" value="fasta"/>
106      <output name="out_file1" file="emboss_transeq_out.fasta"/>
107    </test>
108  </tests>
109  <code file="emboss_format_corrector.py" />
110  <help>
111
112.. class:: warningmark
113
114The input dataset needs to be sequences.
115
116-----
117
118    You can view the original documentation here_.
119   
120    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/transeq.html
121  </help>
122</tool>
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