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

リビジョン 2, 5.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: sirna89" name="sirna" version="5.0.0">
2  <description>Finds siRNA duplexes in mRNA</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>sirna -sequence $input1 -outfile $ofile1 -outseq $ofile2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2
5  -auto</command>
6  <inputs>
7    <param format="fasta" name="input1" type="data">
8      <label>Sequences</label>
9    </param>
10    <param name="poliii" type="select">
11      <label>Select only the 21 base probes that start with a purine (Pol III expression vectors)</label>
12      <option value="no">No</option>
13      <option value="yes">Yes</option>
14    </param>
15    <param name="aa" type="select">
16      <label>Select only those 23 base regions that start with AA</label>
17      <option value="no">No</option>
18      <option value="yes">Yes</option>
19    </param>
20    <param name="tt" type="select">
21      <label>Select only those 23 base regions that end with TT</label>
22      <option value="no">No</option>
23      <option value="yes">Yes</option>
24    </param>
25    <param name="polybase" type="select">
26      <label>Report more than those 23 base regions that have no repeat of 4 or more of any bases in a row</label>
27      <option value="yes">Yes</option>
28      <option value="no">No</option>
29    </param>
30    <param name="context" type="select">
31      <label>Displays the whole 23 bases of the region with the first two bases in brackets</label>
32      <option value="no">No</option>
33      <option value="yes">Yes</option>
34    </param>
35    <param name="out_format1" type="select">
36      <label>Output Report File Format</label>
37      <option value="table">Table</option>
38      <option value="embl">EMBL</option>
39      <option value="genbank">GENBANK</option>
40      <option value="gff">GFF</option>
41      <option value="pir">PIR</option>
42      <option value="swiss">SwissProt</option>
43      <option value="dbmotif">DbMotif</option>
44      <option value="diffseq">Diffseq</option>
45      <option value="excel">Excel (tab delimited)</option>
46      <option value="feattable">FeatTable</option>
47      <option value="motif">Motif</option>
48      <option value="regions">Regions</option>
49      <option value="seqtable">SeqTable</option>
50      <option value="simple">SRS Simple</option>
51      <option value="srs">SRS</option>
52      <option value="tagseq">TagSeq</option>
53    </param>
54    <param name="out_format2" 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="table" name="ofile1" />
89    <data format="fasta" name="ofile2" />
90  </outputs>
91  <tests>
92    <test>
93      <param name="input1" value="2.fasta"/>
94      <param name="poliii" value="no"/>
95      <param name="aa" value="no"/>
96      <param name="tt" value="no"/>
97      <param name="polybase" value="yes"/>
98      <param name="context" value="no"/>
99      <param name="mismatchpercent" value="0"/>
100      <param name="out_format1" value="gff"/>
101      <param name="out_format2" value="fasta"/>
102      <output name="ofile2" file="emboss_sirna_out.fasta"/>
103    </test>
104  </tests>
105  <code file="emboss_format_corrector.py" />
106  <help>
107
108.. class:: warningmark
109
110The input dataset needs to be sequences.
111
112-----
113
114    You can view the original documentation here_.
115   
116    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sirna.html
117  </help>
118</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。