Mercurial > repos > devteam > emboss_5
comparison emboss_seqmatchall.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author | iuc |
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date | Mon, 30 Jan 2017 13:27:40 -0500 |
parents | 9b98d3d903c6 |
children | 27c43fb015f0 |
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10:9b98d3d903c6 | 11:0e2484b6829b |
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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. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ | |
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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ | |
61 </help> | 50 </help> |
51 <expand macro="citations" /> | |
62 </tool> | 52 </tool> |