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comparison emboss_diffseq.xml @ 11:0e2484b6829b draft

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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
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10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0"> 1 <tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0.1">
2 <description>Find differences between nearly identical sequences</description> 2 <description>Find differences between nearly identical sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>diffseq -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize $wordsize -globaldifferences $globaldifferences -rformat3
5 $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command> 9 $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command>
6 <inputs> 10 <inputs>
7 <param format="data" name="input1" type="data"> 11 <param name="input1" type="data" format="data" label="Sequence 1" />
8 <label>Sequence 1</label> 12 <param name="input2" type="data" format="data" label="Sequence 2" />
9 </param> 13 <param name="wordsize" type="integer" value="20" label="Wordsize" />
10 <param format="data" name="input2" type="data"> 14 <param name="globaldifferences" type="select" label="Report differences at the ends">
11 <label>Sequence 2</label>
12 </param>
13 <param name="wordsize" type="text" value="20">
14 <label>Wordsize</label>
15 </param>
16 <param name="globaldifferences" type="select">
17 <label>Report differences at the ends</label>
18 <option value="no">No</option> 15 <option value="no">No</option>
19 <option value="yes">Yes</option> 16 <option value="yes">Yes</option>
20 </param> 17 </param>
21 <param name="out_format1" type="select"> 18 <param name="out_format1" type="select" label="Output report file format">
22 <label>Output Report File Format</label>
23 <option value="diffseq">Diffseq</option> 19 <option value="diffseq">Diffseq</option>
24 <option value="embl">EMBL</option> 20 <option value="embl">EMBL</option>
25 <option value="genbank">GENBANK</option> 21 <option value="genbank">GENBANK</option>
26 <option value="gff">GFF</option> 22 <option value="gff">GFF</option>
27 <option value="pir">PIR</option> 23 <option value="pir">PIR</option>
35 <option value="simple">SRS Simple</option> 31 <option value="simple">SRS Simple</option>
36 <option value="srs">SRS</option> 32 <option value="srs">SRS</option>
37 <option value="table">Table</option> 33 <option value="table">Table</option>
38 <option value="tagseq">TagSeq</option> 34 <option value="tagseq">TagSeq</option>
39 </param> 35 </param>
40 <param name="out_format2" type="select"> 36 <param name="out_format2" type="select" label="Sequence 1 output feature file format">
41 <label>Sequence 1 Output Feature File Format</label>
42 <option value="gff">GFF</option> 37 <option value="gff">GFF</option>
43 <option value="embl">EMBL</option> 38 <option value="embl">EMBL</option>
44 <option value="swiss">SwissProt</option> 39 <option value="swiss">SwissProt</option>
45 </param> 40 </param>
46 <param name="out_format3" type="select"> 41 <param name="out_format3" type="select" label="Sequence 2 output feature file format">
47 <label>Sequence 2 Output Feature File Format</label>
48 <option value="gff">GFF</option> 42 <option value="gff">GFF</option>
49 <option value="embl">EMBL</option> 43 <option value="embl">EMBL</option>
50 <option value="swiss">SwissProt</option> 44 <option value="swiss">SwissProt</option>
51 </param> 45 </param>
52 </inputs> 46 </inputs>
53 <outputs> 47 <outputs>
54 <data format="diffseq" name="out_file1" /> 48 <data name="out_file1" format="diffseq" />
55 <data format="gff" name="out_file2" /> 49 <data name="out_file2" format="gff" />
56 <data format="gff" name="out_file3" /> 50 <data name="out_file3" format="gff" />
57 </outputs> 51 </outputs>
58 <code file="emboss_format_corrector.py" />
59 <help> 52 <help>
60 You can view the original documentation here_. 53 You can view the original documentation here_.
61
62 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/diffseq.html
63 54
64 ------ 55 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/diffseq.html
65
66 **Citation**
67
68 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;`_
69
70 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;`_
71 </help> 56 </help>
57 <expand macro="citations" />
72 </tool> 58 </tool>