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comparison emboss_vectorstrip.xml @ 10:d49956b87f7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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children 8992d258e42f
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="5.0.0.1">
2 <description>Strips out DNA between a pair of vector sequences</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>vectorstrip -sequence '$input1' -vectorsfile '$input2' -outseq '$ofile1' -outfile '$ofile2' -vectorfile yes -mismatch $mismatch -besthits $besthits -linkera '$linkera' -linkerb
9 '$linkerb' -osformat4 $out_format1 -auto</command>
10 <inputs>
11 <param name="input1" type="data" format="fasta" label="Sequences" />
12 <param name="input2" type="data" format="data" label="Vector file" />
13 <param name="mismatch" type="integer" value="10" label="Max allowed percent mismatch" />
14 <param name="besthits" type="select" label="Show only the best hits (minimize mismatches)">
15 <option value="yes">Yes</option>
16 <option value="no">No</option>
17 </param>
18 <param name="linkera" type="text" value="" label="The 5' sequence" />
19 <param name="linkerb" type="text" value="" label="The 3' sequence" />
20 <param name="out_format1" type="select" label="Output sequence file format">
21 <option value="fasta">FASTA (m)</option>
22 <option value="acedb">ACeDB (m)</option>
23 <option value="asn1">ASN.1 (m)</option>
24 <option value="clustal">Clustal (m)</option>
25 <option value="codata">CODATA (m)</option>
26 <option value="embl">EMBL (m)</option>
27 <option value="fitch">Fitch (m)</option>
28 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
29 <option value="genbank">GENBANK (m)</option>
30 <option value="gff">GFF (m)</option>
31 <option value="hennig86">Hennig86 (m)</option>
32 <option value="ig">Intelligenetics (m)</option>
33 <option value="jackknifer">Jackknifer (m)</option>
34 <option value="jackknifernon">Jackknifernon (m)</option>
35 <option value="mega">Mega (m)</option>
36 <option value="meganon">Meganon (m)</option>
37 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
38 <option value="pir">NBRF (PIR) (m)</option>
39 <option value="ncbi">NCBI style FASTA (m)</option>
40 <option value="nexus">Nexus/PAUP (m)</option>
41 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
42 <option value="phylip">PHYLIP interleaved (m)</option>
43 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
44 <option value="selex">SELEX (m)</option>
45 <option value="staden">Staden (s)</option>
46 <option value="strider">DNA strider (m)</option>
47 <option value="swiss">SwisProt entry (m)</option>
48 <option value="text">Plain sequence (s)</option>
49 <option value="treecon">Treecon (m)</option>
50 </param>
51 </inputs>
52 <outputs>
53 <data name="ofile1" format="fasta" />
54 <data name="ofile2" format="vectorstrip" />
55 </outputs>
56 <!-- <tests>
57 <test>
58 <param name="input1" value="1.fasta"/>
59 <param name="input2" value="2.fasta"/>
60 <param name="mismatch" value="10"/>
61 <param name="besthits" value="yes"/>
62 <param name="linkera" value=""/>
63 <param name="linkerb" value=""/>
64 <param name="out_format1" value="fasta"/>
65 <output name="ofile1" file="emboss_vectorstrip_out.fasta"/>
66 </test>
67 </tests> -->
68 <help>
69 You can view the original documentation here_.
70
71 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/vectorstrip.html
72 </help>
73 <expand macro="citations" />
74 </tool>