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comparison emboss_nthseq.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: nthseq62" name="nthseq" version="5.0.0"> 1 <tool id="EMBOSS: nthseq62" name="nthseq" version="5.0.0.1">
2 <description>Writes one sequence from a multiple set of sequences</description> 2 <description>Writes one sequence from a multiple set of sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>nthseq -sequence $input1 -outseq $out_file1 -number $number -osformat2 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>nthseq -sequence '$input1' -outseq '$out_file1' -number $number -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="number" type="integer" value="1" label="Number of the sequence to output" />
8 </param> 12 <param name="out_format1" type="select" label="Output sequence file format">
9 <param name="number" type="text" value="1">
10 <label>Number of the sequence to output</label>
11 </param>
12 <param name="out_format1" type="select">
13 <label>Output Sequence File Format</label>
14 <option value="fasta">FASTA (m)</option> 13 <option value="fasta">FASTA (m)</option>
15 <option value="acedb">ACeDB (m)</option> 14 <option value="acedb">ACeDB (m)</option>
16 <option value="asn1">ASN.1 (m)</option> 15 <option value="asn1">ASN.1 (m)</option>
17 <option value="clustal">Clustal (m)</option> 16 <option value="clustal">Clustal (m)</option>
18 <option value="codata">CODATA (m)</option> 17 <option value="codata">CODATA (m)</option>
41 <option value="text">Plain sequence (s)</option> 40 <option value="text">Plain sequence (s)</option>
42 <option value="treecon">Treecon (m)</option> 41 <option value="treecon">Treecon (m)</option>
43 </param> 42 </param>
44 </inputs> 43 </inputs>
45 <outputs> 44 <outputs>
46 <data format="fasta" name="out_file1" /> 45 <data name="out_file1" format="fasta" />
47 </outputs> 46 </outputs>
48 <tests> 47 <tests>
49 <test> 48 <test>
50 <param name="input1" value="2.fasta"/> 49 <param name="input1" value="2.fasta"/>
51 <param name="number" value="1"/> 50 <param name="number" value="1"/>
52 <param name="out_format1" value="fasta"/> 51 <param name="out_format1" value="fasta"/>
53 <output name="out_file1" file="emboss_nthseq_out.fasta"/> 52 <output name="out_file1" file="emboss_nthseq_out.fasta"/>
54 </test> 53 </test>
55 </tests> 54 </tests>
56 <code file="emboss_format_corrector.py" />
57 <help> 55 <help>
58
59 .. class:: warningmark 56 .. class:: warningmark
60 57
61 The input dataset needs to be sequences. 58 The input dataset needs to be sequences.
62 59
63 ----- 60 -----
64 61
65 You can view the original documentation here_. 62 You can view the original documentation here_.
66
67 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/nthseq.html
68 63
69 ------ 64 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/nthseq.html
70
71 **Citation**
72
73 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;`_
74
75 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;`_
76 </help> 65 </help>
66 <expand macro="citations" />
77 </tool> 67 </tool>