comparison emboss_sirna.xml @ 10:9b98d3d903c6 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
parents
children 0e2484b6829b
comparison
equal deleted inserted replaced
9:18a63c800a4d 10:9b98d3d903c6
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
110 The 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
118 ------
119
120 **Citation**
121
122 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
123
124 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
125 </help>
126 </tool>