comparison emboss_megamerger.xml @ 11:0e2484b6829b draft

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: megamerger53" name="megamerger" version="5.0.0"> 1 <tool id="EMBOSS: megamerger53" name="megamerger" version="5.0.0.1">
2 <description>Merge two large overlapping nucleic acid sequences</description> 2 <description>Merge two large overlapping nucleic acid sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>megamerger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -wordsize $wordsize -prefer $prefer -osformat3 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>megamerger -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -outfile '$out_file2' -wordsize $wordsize -prefer $prefer -osformat3 $out_format1 -auto</command>
5 <inputs> 9 <inputs>
6 <param format="data" name="input1" type="data"> 10 <param name="input1" type="data" format="data" label="Sequence 1" />
7 <label>Sequence 1</label> 11 <param name="input2" type="data" format="data" label="Sequence 2" />
8 </param> 12 <param name="wordsize" type="integer" value="20" label="Word size" />
9 <param format="data" name="input2" type="data"> 13 <param name="prefer" type="select" label="Prefer first sequence when mismatches occur">
10 <label>Sequence 2</label>
11 </param>
12 <param name="wordsize" type="text" value="20">
13 <label>Word size</label>
14 </param>
15 <param name="prefer" type="select">
16 <label>Prefer first sequence when mismatches occur</label>
17 <option value="no">No</option> 14 <option value="no">No</option>
18 <option value="yes">Yes</option> 15 <option value="yes">Yes</option>
19 </param> 16 </param>
20 <param name="out_format1" type="select"> 17 <param name="out_format1" type="select" label="Output sequence file format">
21 <label>Output Sequence File Format</label>
22 <option value="fasta">FASTA (m)</option> 18 <option value="fasta">FASTA (m)</option>
23 <option value="acedb">ACeDB (m)</option> 19 <option value="acedb">ACeDB (m)</option>
24 <option value="asn1">ASN.1 (m)</option> 20 <option value="asn1">ASN.1 (m)</option>
25 <option value="clustal">Clustal (m)</option> 21 <option value="clustal">Clustal (m)</option>
26 <option value="codata">CODATA (m)</option> 22 <option value="codata">CODATA (m)</option>
49 <option value="text">Plain sequence (s)</option> 45 <option value="text">Plain sequence (s)</option>
50 <option value="treecon">Treecon (m)</option> 46 <option value="treecon">Treecon (m)</option>
51 </param> 47 </param>
52 </inputs> 48 </inputs>
53 <outputs> 49 <outputs>
54 <data format="fasta" name="out_file1" /> 50 <data name="out_file1" format="fasta" />
55 <data format="txt" name="out_file2" /> 51 <data name="out_file2" format="txt" />
56 </outputs> 52 </outputs>
57 <code file="emboss_format_corrector.py" />
58 <help> 53 <help>
59 You can view the original documentation here_. 54 You can view the original documentation here_.
60
61 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/megamerger.html
62 55
63 ------ 56 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/megamerger.html
64
65 **Citation**
66
67 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;`_
68
69 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;`_
70 </help> 57 </help>
58 <expand macro="citations" />
71 </tool> 59 </tool>