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

リビジョン 2, 4.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0">
2  <description>Protein pattern search after translation</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
5  <inputs>
6    <param format="fasta" name="input1" type="data">
7      <label>Sequences</label>
8    </param>
9    <param name="pattern" size="5" type="text" value="">
10      <label>Search pattern</label>
11    </param>
12    <param name="mismatch" size="5" type="text" value="0">
13      <label>Number of mismatches</label>
14    </param>
15    <param name="frame" type="select">
16      <label>Frame(s) to translate</label>
17      <option value="1">Frame 1</option>
18      <option value="2">Frame 2</option>
19      <option value="3">Frame 3</option>
20      <option value="F">Forward three frames</option>
21      <option value="-1">Frame -1</option>
22      <option value="-2">Frame -2</option>
23      <option value="-3">Frame -3</option>
24      <option value="R">Reverse three frames</option>
25      <option value="6">All six frames</option>
26    </param>
27    <param name="table" type="select">
28      <label>Code to use</label>
29      <option value="0">Standard</option>
30      <option value="1">Standard (with alternative initiation codons)</option>
31      <option value="2">Vertebrate Mitochondrial</option>
32      <option value="3">Yeast Mitochondrial</option>
33      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
34      <option value="5">Invertebrate Mitochondrial</option>
35      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
36      <option value="9">Echinoderm Mitochondrial</option>
37      <option value="10">Euplotid Nuclear</option>
38      <option value="11">Bacterial</option>
39      <option value="12">Alternative Yeast Nuclear</option>
40      <option value="13">Ascidian Mitochondrial</option>
41      <option value="14">Flatworm Mitochondrial</option>
42      <option value="15">Blepharisma Macronuclear</option>
43      <option value="16">Chlorophycean Mitochondrial</option>
44      <option value="21">Trematode Mitochondrial</option>
45      <option value="22">Scenedesmus obliquus</option>
46      <option value="23">Thraustochytrium Mitochondrial</option>
47    </param>
48    <param name="out_format1" type="select">
49      <label>Output Report File Format</label>
50      <option value="table">Table</option>
51      <option value="embl">EMBL</option>
52      <option value="genbank">GENBANK</option>
53      <option value="gff">GFF</option>
54      <option value="pir">PIR</option>
55      <option value="swiss">SwissProt</option>
56      <option value="dbmotif">DbMotif</option>
57      <option value="diffseq">Diffseq</option>
58      <option value="excel">Excel (tab delimited)</option>
59      <option value="feattable">FeatTable</option>
60      <option value="motif">Motif</option>
61      <option value="regions">Regions</option>
62      <option value="seqtable">SeqTable</option>
63      <option value="simple">SRS Simple</option>
64      <option value="srs">SRS</option>
65      <option value="tagseq">TagSeq</option>
66    </param>
67  </inputs>
68  <outputs>
69    <data format="fuzztran" name="out_file1" />
70  </outputs>
71  <tests>
72    <test>
73      <param name="input1" value="1.fasta"/>
74      <param name="pattern" value="AA"/>
75      <param name="mismatch" value="0"/>
76      <param name="frame" value="6"/>
77      <param name="table" value="0"/>
78      <param name="out_format1" value="excel"/>
79      <output name="out_file1" file="emboss_fuzztran_out.tabular"/>
80    </test>
81  </tests>
82  <code file="emboss_format_corrector.py" />
83  <help>
84
85.. class:: warningmark
86
87The input dataset needs to be sequences.
88
89-----
90
91    You can view the original documentation here_.
92   
93    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzztran.html
94  </help>
95</tool>
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