Mercurial > repos > devteam > emboss_5

comparison emboss_seqmatchall.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: seqmatchall83" name="seqmatchall" version="5.0.0"> 1 <tool id="EMBOSS: seqmatchall83" name="seqmatchall" version="5.0.0.1">
2 <description>All-against-all comparison of a set of sequences</description> 2 <description>All-against-all comparison of a set of sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>seqmatchall -sequence $input1 -outfile $out_file1 -wordsize $wordsize -aformat2 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>seqmatchall -sequence '$input1' -outfile '$out_file1' -wordsize $wordsize -aformat2 $out_format1 -auto</command>
5 <inputs> 9 <inputs>
6 <param format="fasta" name="input1" type="data"> 10 <param name="input1" type="data" format="fasta" label="Sequences" />
7 <label>Sequences</label> 11 <param name="wordsize" type="integer" value="4" label="Word size" />
8 </param> 12 <param name="out_format1" type="select" label="Output alignment file format">
9 <param name="wordsize" type="text" value="4">
10 <label>Word size</label>
11 </param>
12 <param name="out_format1" type="select">
13 <label>Output Alignment File Format</label>
14 <option value="match">Match (m)</option> 13 <option value="match">Match (m)</option>
15 <option value="simple">Simple (m)</option> 14 <option value="simple">Simple (m)</option>
16 <option value="fasta">FASTA (m)</option> 15 <option value="fasta">FASTA (m)</option>
17 <option value="msf">MSF (m)</option> 16 <option value="msf">MSF (m)</option>
18 <option value="srs">SRS (m)</option> 17 <option value="srs">SRS (m)</option>
26 <option value="score">Score (p)</option> 25 <option value="score">Score (p)</option>
27 <option value="seqmatchall">Seqmatchall Output File</option> 26 <option value="seqmatchall">Seqmatchall Output File</option>
28 </param> 27 </param>
29 </inputs> 28 </inputs>
30 <outputs> 29 <outputs>
31 <data format="seqmatchall" name="out_file1" />. 30 <data name="out_file1" format="seqmatchall" />
32 </outputs> 31 </outputs>
33 <tests> 32 <tests>
34 <test> 33 <test>
35 <param name="input1" value="2.fasta"/> 34 <param name="input1" value="2.fasta"/>
36 <param name="wordsize" value="2"/> 35 <param name="wordsize" value="2"/>
37 <param name="out_format1" value="fasta"/> 36 <param name="out_format1" value="fasta"/>
38 <output name="out_file1" file="emboss_seqmatchall_out.fasta"/> 37 <output name="out_file1" file="emboss_seqmatchall_out.fasta"/>
39 </test> 38 </test>
40 </tests> 39 </tests>
41 <code file="emboss_format_corrector.py" />
42 <help> 40 <help>
43
44 .. class:: warningmark 41 .. class:: warningmark
45 42
46 The input dataset needs to be sequences. 43 The input dataset needs to be sequences.
47 44
48 ----- 45 -----
49 46
50 You can view the original documentation here_. 47 You can view the original documentation here_.
51
52 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/seqmatchall.html
53 48
54 ------ 49 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/seqmatchall.html
55
56 **Citation**
57
58 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;`_
59
60 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;`_
61 </help> 50 </help>
51 <expand macro="citations" />
62 </tool> 52 </tool>