root/galaxy-central/tools/emboss_5/emboss_getorf.xml

リビジョン 2, 5.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: getorf42" name="getorf" version="5.0.0">
2  <description>Finds and extracts open reading frames (ORFs)</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>getorf -sequence $input1 -outseq $out_file1 -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking
5  -osformat2 $out_format1 -auto</command>
6  <inputs>
7    <param format="fasta" name="input1" type="data">
8      <label>Sequences</label>
9    </param>
10    <param name="table" type="select">
11      <label>Code to use</label>
12      <option value="0">Standard</option>
13      <option value="1">Standard (with alternative initiation codons)</option>
14      <option value="2">Vertebrate Mitochondrial</option>
15      <option value="3">Yeast Mitochondrial</option>
16      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
17      <option value="5">Invertebrate Mitochondrial</option>
18      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
19      <option value="9">Echinoderm Mitochondrial</option>
20      <option value="10">Euplotid Nuclear</option>
21      <option value="11">Bacterial</option>
22      <option value="12">Alternative Yeast Nuclear</option>
23      <option value="13">Ascidian Mitochondrial</option>
24      <option value="14">Flatworm Mitochondrial</option>
25      <option value="15">Blepharisma Macronuclear</option>
26      <option value="16">Chlorophycean Mitochondrial</option>
27      <option value="21">Trematode Mitochondrial</option>
28      <option value="22">Scenedesmus obliquus</option>
29      <option value="23">Thraustochytrium Mitochondrial</option>
30    </param>
31    <param name="minsize" size="10" type="text" value="30">
32      <label>Minimum nucleotide size of ORF to report</label>
33    </param>
34    <param name="maxsize" size="10" type="text" value="1000000">
35      <label>Maximum nucleotide size of ORF to report</label>
36    </param>
37    <param name="find" type="select">
38      <label>What to output</label>
39      <option value="0">Translation of regions between STOP codons</option>
40      <option value="1">Translation of regions between START and STOP codons</option>
41      <option value="2">Nucleic sequences between STOP codons</option>
42      <option value="3">Nucleic sequences between START and STOP codons</option>
43      <option value="4">Nucleotides flanking START codons</option>
44      <option value="5">Nucleotides flanking initial STOP codons</option>
45      <option value="6">Nucleotides flanking ending STOP codons</option>
46    </param>
47    <param name="methionine" type="select">
48      <label>All START codons to code for Methionine</label>
49      <option value="yes">Yes</option>
50      <option value="no">No</option>
51    </param>
52    <param name="circular" type="select">
53      <label>Circular sequence</label>
54      <option value="no">No</option>
55      <option value="yes">Yes</option>
56    </param>
57    <param name="reverse" type="select">
58      <label>Find ORFs in the reverse complement</label>
59      <option value="yes">Yes</option>
60      <option value="no">No</option>
61    </param>
62    <param name="flanking" size="10" type="text" value="100">
63      <label>Number of flanking nucleotides to output</label>
64    </param>
65    <param name="out_format1" type="select">
66      <label>Output Sequence File Format</label>
67      <option value="fasta">FASTA (m)</option>
68      <option value="acedb">ACeDB (m)</option>
69      <option value="asn1">ASN.1 (m)</option>
70      <option value="clustal">Clustal (m)</option>
71      <option value="codata">CODATA (m)</option>
72      <option value="embl">EMBL (m)</option>
73      <option value="fitch">Fitch (m)</option>
74      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
75      <option value="genbank">GENBANK (m)</option>
76      <!-- <option value="gff">GFF (m)</option> -->
77      <option value="hennig86">Hennig86 (m)</option>
78      <option value="ig">Intelligenetics (m)</option>
79      <option value="jackknifer">Jackknifer (m)</option>
80      <option value="jackknifernon">Jackknifernon (m)</option>
81      <option value="mega">Mega (m)</option>
82      <option value="meganon">Meganon (m)</option>
83      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
84      <option value="pir">NBRF (PIR) (m)</option>
85      <option value="ncbi">NCBI style FASTA (m)</option>
86      <option value="nexus">Nexus/PAUP (m)</option>
87      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
88      <option value="phylip">PHYLIP interleaved (m)</option>
89      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
90      <option value="selex">SELEX (m)</option>
91      <option value="staden">Staden (s)</option>
92      <option value="strider">DNA strider (m)</option>
93      <option value="swiss">SwisProt entry (m)</option>
94      <option value="text">Plain sequence (s)</option>
95      <option value="treecon">Treecon (m)</option>
96    </param>
97  </inputs>
98  <outputs>
99    <data format="fasta" name="out_file1" />
100  </outputs>
101  <tests>
102    <test>
103      <param name="input1" value="2.fasta"/>
104      <param name="minsize" value="30"/>
105      <param name="maxsize" value="1000000"/>
106      <param name="find" value="0"/>
107      <param name="methionine" value="yes"/>
108      <param name="circular" value="no"/>
109      <param name="reverse" value="yes"/>
110      <param name="table" value="0"/>
111      <param name="flanking" value="100"/>
112      <param name="out_format1" value="fasta"/>
113      <output name="out_file1" file="emboss_getorf_out.fasta"/>
114    </test>
115  </tests>
116  <code file="emboss_format_corrector.py" />
117  <help>
118
119.. class:: warningmark
120
121The input dataset needs to be sequences.
122
123-----
124
125    You can view the original documentation here_.
126   
127    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.html
128  </help>
129</tool>
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