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comparison emboss_revseq.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: revseq82" name="revseq" version="5.0.0"> 1 <tool id="EMBOSS: revseq82" name="revseq" version="5.0.0">
2 <description>Reverse and complement a sequence</description> 2 <description>Reverse and complement a sequence</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>revseq -sequence $input1 -outseq $out_file1 -reverse $reverse -complement $complement -osformat2 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>revseq -sequence '$input1' -outseq '$out_file1' -reverse $reverse -complement $complement -osformat2 $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="reverse" type="select" label="Reverse the sequence">
8 </param>
9 <param name="reverse" type="select">
10 <label>Reverse the sequence</label>
11 <option value="yes">Yes</option> 12 <option value="yes">Yes</option>
12 <option value="no">No</option> 13 <option value="no">No</option>
13 </param> 14 </param>
14 <param name="complement" type="select"> 15 <param name="complement" type="select" label="Complement the sequence">
15 <label>Complement the sequence</label>
16 <option value="yes">Yes</option> 16 <option value="yes">Yes</option>
17 <option value="no">No</option> 17 <option value="no">No</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="reverse" value="yes"/> 57 <param name="reverse" value="yes"/>
59 <param name="complement" value="yes"/> 58 <param name="complement" value="yes"/>
60 <param name="out_format1" value="fasta"/> 59 <param name="out_format1" value="fasta"/>
61 <output name="out_file1" file="emboss_revseq_out.fasta"/> 60 <output name="out_file1" file="emboss_revseq_out.fasta"/>
62 </test> 61 </test>
63 </tests> 62 </tests>
64 <code file="emboss_format_corrector.py" />
65 <help> 63 <help>
66
67 .. class:: warningmark 64 .. class:: warningmark
68 65
69 The input dataset needs to be sequences. 66 The input dataset needs to be sequences.
70 67
71 ----- 68 -----
72 69
73 You can view the original documentation here_. 70 You can view the original documentation here_.
74
75 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/revseq.html
76 71
77 ------ 72 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/revseq.html
78
79 **Citation**
80
81 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;`_
82
83 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;`_
84 </help> 73 </help>
74 <expand macro="citations" />
85 </tool> 75 </tool>