Mercurial > repos > devteam > emboss_5
comparison emboss_seqret.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: seqret84" name="seqret" version="5.0.0"> | 1 <tool id="EMBOSS: seqret84" name="seqret" version="5.0.0"> |
2 <description>Reads and writes sequences</description> | 2 <description>Reads and writes sequences</description> |
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | 3 <macros> |
4 <command>seqret -sequence $input1 -outseq $out_file1 -feature $feature -firstonly $firstonly -osformat2 $out_format1 -auto</command> | 4 <import>macros.xml</import> |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <code file="emboss_format_corrector.py" /> | |
8 <command>seqret -sequence '$input1' -outseq '$out_file1' -feature $feature -firstonly $firstonly -osformat2 $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="Sequences" /> |
7 <label>Sequences</label> | 11 <param name="feature" type="select" label="Use feature information"> |
8 </param> | |
9 <param name="feature" type="select"> | |
10 <label>Use feature information</label> | |
11 <option value="no">No</option> | 12 <option value="no">No</option> |
12 <option value="yes">Yes</option> | 13 <option value="yes">Yes</option> |
13 </param> | 14 </param> |
14 <param name="firstonly" type="select"> | 15 <param name="firstonly" type="select" label="Read one sequence and stop"> |
15 <label>Read one sequence and stop</label> | |
16 <option value="no">No</option> | 16 <option value="no">No</option> |
17 <option value="yes">Yes</option> | 17 <option value="yes">Yes</option> |
18 </param> | 18 </param> |
19 <param name="out_format1" type="select"> | 19 <param name="out_format1" type="select" label="Output sequence file format"> |
20 <label>Output Sequence File Format</label> | |
21 <option value="fasta">FASTA (m)</option> | 20 <option value="fasta">FASTA (m)</option> |
22 <option value="acedb">ACeDB (m)</option> | 21 <option value="acedb">ACeDB (m)</option> |
23 <option value="asn1">ASN.1 (m)</option> | 22 <option value="asn1">ASN.1 (m)</option> |
24 <option value="clustal">Clustal (m)</option> | 23 <option value="clustal">Clustal (m)</option> |
25 <option value="codata">CODATA (m)</option> | 24 <option value="codata">CODATA (m)</option> |
48 <option value="text">Plain sequence (s)</option> | 47 <option value="text">Plain sequence (s)</option> |
49 <option value="treecon">Treecon (m)</option> | 48 <option value="treecon">Treecon (m)</option> |
50 </param> | 49 </param> |
51 </inputs> | 50 </inputs> |
52 <outputs> | 51 <outputs> |
53 <data format="fasta" name="out_file1" /> | 52 <data name="out_file1" format="fasta" /> |
54 </outputs> | 53 </outputs> |
55 <tests> | 54 <tests> |
56 <test> | 55 <test> |
57 <param name="input1" value="2.fasta"/> | 56 <param name="input1" value="2.fasta"/> |
58 <param name="feature" value="no"/> | 57 <param name="feature" value="no"/> |
59 <param name="firstonly" value="no"/> | 58 <param name="firstonly" value="no"/> |
60 <param name="out_format1" value="fasta"/> | 59 <param name="out_format1" value="fasta"/> |
61 <output name="out_file1" file="emboss_seqret_out.fasta"/> | 60 <output name="out_file1" file="emboss_seqret_out.fasta"/> |
62 </test> | 61 </test> |
63 </tests> | 62 </tests> |
64 <code file="emboss_format_corrector.py" /> | |
65 <help> | 63 <help> |
66 You can view the original documentation here_. | 64 You can view the original documentation here_. |
67 | |
68 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/seqret.html | |
69 | 65 |
70 ------ | 66 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/seqret.html |
71 | |
72 **Citation** | |
73 | |
74 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>`_ | |
75 | |
76 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>`_ | |
77 </help> | 67 </help> |
68 <expand macro="citations" /> | |
78 </tool> | 69 </tool> |