Mercurial > repos > devteam > emboss_5

comparison emboss_vectorstrip.xml @ 11:0e2484b6829b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
comparison
equal deleted inserted replaced
10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="5.0.0"> 1 <tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="5.0.0.1">
2 <description>Strips out DNA between a pair of vector sequences</description> 2 <description>Strips out DNA between a pair of vector sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>vectorstrip -sequence $input1 -vectorsfile $input2 -outseq $ofile1 -outfile $ofile2 -vectorfile yes -mismatch "$mismatch" -besthits $besthits -linkera "$linkera" -linkerb 4 <import>macros.xml</import>
5 "$linkerb" -osformat4 $out_format1 -auto</command> 5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>vectorstrip -sequence '$input1' -vectorsfile '$input2' -outseq '$ofile1' -outfile '$ofile2' -vectorfile yes -mismatch $mismatch -besthits $besthits -linkera '$linkera' -linkerb
9 '$linkerb' -osformat4 $out_format1 -auto</command>
6 <inputs> 10 <inputs>
7 <param format="fasta" name="input1" type="data"> 11 <param name="input1" type="data" format="fasta" label="Sequences" />
8 <label>Sequences</label> 12 <param name="input2" type="data" format="data" label="Vector file" />
9 </param> 13 <param name="mismatch" type="integer" value="10" label="Max allowed percent mismatch" />
10 <param format="data" name="input2" type="data"> 14 <param name="besthits" type="select" label="Show only the best hits (minimize mismatches)">
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> 15 <option value="yes">Yes</option>
19 <option value="no">No</option> 16 <option value="no">No</option>
20 </param> 17 </param>
21 <param name="linkera" type="text" value=""> 18 <param name="linkera" type="text" value="" label="The 5' sequence" />
22 <label>The 5' sequence</label> 19 <param name="linkerb" type="text" value="" label="The 3' sequence" />
23 </param> 20 <param name="out_format1" type="select" label="Output sequence file format">
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> 21 <option value="fasta">FASTA (m)</option>
30 <option value="acedb">ACeDB (m)</option> 22 <option value="acedb">ACeDB (m)</option>
31 <option value="asn1">ASN.1 (m)</option> 23 <option value="asn1">ASN.1 (m)</option>
32 <option value="clustal">Clustal (m)</option> 24 <option value="clustal">Clustal (m)</option>
33 <option value="codata">CODATA (m)</option> 25 <option value="codata">CODATA (m)</option>
56 <option value="text">Plain sequence (s)</option> 48 <option value="text">Plain sequence (s)</option>
57 <option value="treecon">Treecon (m)</option> 49 <option value="treecon">Treecon (m)</option>
58 </param> 50 </param>
59 </inputs> 51 </inputs>
60 <outputs> 52 <outputs>
61 <data format="fasta" name="ofile1" /> 53 <data name="ofile1" format="fasta" />
62 <data format="vectorstrip" name="ofile2" /> 54 <data name="ofile2" format="vectorstrip" />
63 </outputs> 55 </outputs>
64 <!-- <tests> 56 <!-- <tests>
65 <test> 57 <test>
66 <param name="input1" value="1.fasta"/> 58 <param name="input1" value="1.fasta"/>
67 <param name="input2" value="2.fasta"/> 59 <param name="input2" value="2.fasta"/>
71 <param name="linkerb" value=""/> 63 <param name="linkerb" value=""/>
72 <param name="out_format1" value="fasta"/> 64 <param name="out_format1" value="fasta"/>
73 <output name="ofile1" file="emboss_vectorstrip_out.fasta"/> 65 <output name="ofile1" file="emboss_vectorstrip_out.fasta"/>
74 </test> 66 </test>
75 </tests> --> 67 </tests> -->
76 <code file="emboss_format_corrector.py" />
77 <help> 68 <help>
78 You can view the original documentation here_. 69 You can view the original documentation here_.
79
80 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/vectorstrip.html
81 70
82 ------ 71 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/vectorstrip.html
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> 72 </help>
73 <expand macro="citations" />
90 </tool> 74 </tool>