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comparison emboss_vectorstrip.xml @ 10:9b98d3d903c6 draft

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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
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9:18a63c800a4d 10:9b98d3d903c6
1 <tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="5.0.0">
2 <description>Strips out DNA between a pair of vector sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>vectorstrip -sequence $input1 -vectorsfile $input2 -outseq $ofile1 -outfile $ofile2 -vectorfile yes -mismatch "$mismatch" -besthits $besthits -linkera "$linkera" -linkerb
5 "$linkerb" -osformat4 $out_format1 -auto</command>
6 <inputs>
7 <param format="fasta" name="input1" type="data">
8 <label>Sequences</label>
9 </param>
10 <param format="data" name="input2" type="data">
11 <label>Vector file</label>
12 </param>
13 <param name="mismatch" type="text" value="10">
14 <label>Max allowed percent mismatch</label>
15 </param>
16 <param name="besthits" type="select">
17 <label>Show only the best hits (minimize mismatches)</label>
18 <option value="yes">Yes</option>
19 <option value="no">No</option>
20 </param>
21 <param name="linkera" type="text" value="">
22 <label>The 5' sequence</label>
23 </param>
24 <param name="linkerb" type="text" value="">
25 <label>The 3' sequence</label>
26 </param>
27 <param name="out_format1" type="select">
28 <label>Output Sequence File Format</label>
29 <option value="fasta">FASTA (m)</option>
30 <option value="acedb">ACeDB (m)</option>
31 <option value="asn1">ASN.1 (m)</option>
32 <option value="clustal">Clustal (m)</option>
33 <option value="codata">CODATA (m)</option>
34 <option value="embl">EMBL (m)</option>
35 <option value="fitch">Fitch (m)</option>
36 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
37 <option value="genbank">GENBANK (m)</option>
38 <option value="gff">GFF (m)</option>
39 <option value="hennig86">Hennig86 (m)</option>
40 <option value="ig">Intelligenetics (m)</option>
41 <option value="jackknifer">Jackknifer (m)</option>
42 <option value="jackknifernon">Jackknifernon (m)</option>
43 <option value="mega">Mega (m)</option>
44 <option value="meganon">Meganon (m)</option>
45 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
46 <option value="pir">NBRF (PIR) (m)</option>
47 <option value="ncbi">NCBI style FASTA (m)</option>
48 <option value="nexus">Nexus/PAUP (m)</option>
49 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
50 <option value="phylip">PHYLIP interleaved (m)</option>
51 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
52 <option value="selex">SELEX (m)</option>
53 <option value="staden">Staden (s)</option>
54 <option value="strider">DNA strider (m)</option>
55 <option value="swiss">SwisProt entry (m)</option>
56 <option value="text">Plain sequence (s)</option>
57 <option value="treecon">Treecon (m)</option>
58 </param>
59 </inputs>
60 <outputs>
61 <data format="fasta" name="ofile1" />
62 <data format="vectorstrip" name="ofile2" />
63 </outputs>
64 <!-- <tests>
65 <test>
66 <param name="input1" value="1.fasta"/>
67 <param name="input2" value="2.fasta"/>
68 <param name="mismatch" value="10"/>
69 <param name="besthits" value="yes"/>
70 <param name="linkera" value=""/>
71 <param name="linkerb" value=""/>
72 <param name="out_format1" value="fasta"/>
73 <output name="ofile1" file="emboss_vectorstrip_out.fasta"/>
74 </test>
75 </tests> -->
76 <code file="emboss_format_corrector.py" />
77 <help>
78 You can view the original documentation here_.
79
80 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/vectorstrip.html
81
82 ------
83
84 **Citation**
85
86 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;`_
87
88 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;`_
89 </help>
90 </tool>