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

リビジョン 2, 7.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1<tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0">
2  <!-- tool adds file description and timestamp to output data -->
3  <description>Display a DNA sequence with 6-frame translation and ORFs</description>
4  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
5  <command>sixpack -sequence $input1 -outfile $ofile1 -outseq $ofile2 -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase
6  "$uppercase" -number $number -width "$width" -length "$length" -margin "$margin" -name $disp_name -description $description -offset "$offset" -html $html_out1 -osformat $out_format2 -auto</command>
7  <inputs>
8    <param format="fasta" name="input1" type="data">
9      <label>Sequences</label>
10    </param>
11    <param name="table" type="select">
12      <label>Code to use</label>
13      <option value="0">Standard</option>
14      <option value="1">Standard (with alternative initiation codons)</option>
15      <option value="2">Vertebrate Mitochondrial</option>
16      <option value="3">Yeast Mitochondrial</option>
17      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
18      <option value="5">Invertebrate Mitochondrial</option>
19      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
20      <option value="9">Echinoderm Mitochondrial</option>
21      <option value="10">Euplotid Nuclear</option>
22      <option value="11">Bacterial</option>
23      <option value="12">Alternative Yeast Nuclear</option>
24      <option value="13">Ascidian Mitochondrial</option>
25      <option value="14">Flatworm Mitochondrial</option>
26      <option value="15">Blepharisma Macronuclear</option>
27      <option value="16">Chlorophycean Mitochondrial</option>
28      <option value="21">Trematode Mitochondrial</option>
29      <option value="22">Scenedesmus obliquus</option>
30      <option value="23">Thraustochytrium Mitochondrial</option>
31    </param>
32    <param name="firstorf" type="select">
33      <label>Count the beginning of a sequence as a possible ORF</label>
34      <option value="yes">Yes</option>
35      <option value="no">No</option>
36    </param>
37    <param name="lastorf" type="select">
38      <label>Count the end of a sequence as a possible ORF</label>
39      <option value="yes">Yes</option>
40      <option value="no">No</option>
41    </param>
42    <param name="mstart" type="select">
43      <label>Displays only ORFs starting with an M</label>
44      <option value="no">No</option>
45      <option value="yes">Yes</option>
46    </param>
47    <param name="reverse" type="select">
48      <label>Display the translation of the DNA sequence in the 3 reverse frames</label>
49      <option value="yes">Yes</option>
50      <option value="no">No</option>
51    </param>
52    <param name="orfminsize" size="4" type="text" value="1">
53      <label>Minimum size of Open Reading Frames (ORFs) to display in the translations</label>
54    </param>
55    <param name="uppercase" size="50" type="text" value="">
56      <label>Regions to put in uppercase</label>
57    </param>
58    <param name="number" type="select">
59      <label>Number the sequence at the beginning and the end of each line</label>
60      <option value="yes">Yes</option>
61      <option value="no">No</option>
62    </param>
63    <param name="width" size="4" type="text" value="60">
64      <label>Number of nucleotides displayed on each line</label>
65    </param>
66    <param name="length" size="4" type="text" value="0">
67      <label>Line length of page</label>
68    </param>
69    <param name="margin" size="4" type="text" value="10">
70      <label>Margin around sequence for numbering</label>
71    </param>
72    <param name="disp_name" type="select">
73      <label>Display the ID name of the sequence</label>
74      <option value="yes">Yes</option>
75      <option value="no">No</option>
76    </param>
77    <param name="description" type="select">
78      <label>Display the description of the sequence</label>
79      <option value="yes">Yes</option>
80      <option value="no">No</option>
81    </param>
82    <param name="offset" size="4" type="text" value="1">
83      <label>Number from which you want the DNA sequence to be numbered</label>
84    </param>
85    <param name="html_out1" type="select">
86      <label>Format output as an HTML table</label>
87      <option value="no">No</option>
88      <option value="yes">Yes</option>
89    </param>
90    <param name="out_format2" type="select">
91      <label>Output Sequence File Format</label>
92      <option value="fasta">FASTA (m)</option>
93      <option value="acedb">ACeDB (m)</option>
94      <option value="asn1">ASN.1 (m)</option>
95      <option value="clustal">Clustal (m)</option>
96      <option value="codata">CODATA (m)</option>
97      <option value="embl">EMBL (m)</option>
98      <option value="fitch">Fitch (m)</option>
99      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
100      <option value="genbank">GENBANK (m)</option>
101      <option value="gff">GFF (m)</option>
102      <option value="hennig86">Hennig86 (m)</option>
103      <option value="ig">Intelligenetics (m)</option>
104      <option value="jackknifer">Jackknifer (m)</option>
105      <option value="jackknifernon">Jackknifernon (m)</option>
106      <option value="mega">Mega (m)</option>
107      <option value="meganon">Meganon (m)</option>
108      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
109      <option value="pir">NBRF (PIR) (m)</option>
110      <option value="ncbi">NCBI style FASTA (m)</option>
111      <option value="nexus">Nexus/PAUP (m)</option>
112      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
113      <option value="phylip">PHYLIP interleaved (m)</option>
114      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
115      <option value="selex">SELEX (m)</option>
116      <option value="staden">Staden (s)</option>
117      <option value="strider">DNA strider (m)</option>
118      <option value="swiss">SwisProt entry (m)</option>
119      <option value="text">Plain sequence (s)</option>
120      <option value="treecon">Treecon (m)</option>
121    </param>
122  </inputs>
123  <outputs>
124    <data format="sixpack" name="ofile1" />
125    <data format="fasta" name="ofile2" />
126  </outputs>
127<!--    <tests>
128    <test>
129      <param name="input1" value="2.fasta"/>
130      <param name="table" value="0"/>
131      <param name="firstorf" value="no"/>
132      <param name="lastorf" value="no"/>
133      <param name="mstart" value="no"/>
134      <param name="reverse" value="no"/>
135      <param name="orfminsize" value="1"/>
136      <param name="uppercase" value=""/>
137      <param name="number" value="no"/>
138      <param name="width" value="60"/>
139      <param name="length" value="0"/>
140      <param name="margin" value="10"/>
141      <param name="disp_name" value="no"/>
142      <param name="description" value="no"/>
143      <param name="offset" value="1"/>
144      <param name="html_out1" value="no"/>
145      <param name="out_format2" value="fasta"/>
146      <output name="ofile2" file="emboss_sixpack_out.fasta"/>
147    </test>
148  </tests> -->
149  <code file="emboss_format_corrector.py" />
150  <help>
151
152.. class:: warningmark
153
154The input dataset needs to be sequences.
155
156-----
157
158    You can view the original documentation here_.
159   
160    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sixpack.html
161  </help>
162</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。