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comparison emboss_extractseq.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: extractseq35" name="extractseq" version="5.0.0"> 1 <tool id="EMBOSS: extractseq35" name="extractseq" version="5.0.0">
2 <description>Extract regions from a sequence</description> 2 <description>Extract regions from a sequence</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>extractseq -sequence $input1 -outseq $out_file1 -regions $regions -separate $separate -osformat2 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>extractseq -sequence '$input1' -outseq '$out_file1' -regions '$regions' -separate $separate -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="regions" type="text" value="1-9999999" label="Regions to extract" />
8 </param> 12 <param name="separate" type="select" label="Write each specified region as a separate sequence">
9 <param name="regions" type="text" value="1-9999999">
10 <label>Regions to extract</label>
11 </param>
12 <param name="separate" type="select">
13 <label>Write each specified region as a separate sequence</label>
14 <option value="no">No</option> 13 <option value="no">No</option>
15 <option value="yes">Yes</option> 14 <option value="yes">Yes</option>
16 </param> 15 </param>
17 <param name="out_format1" type="select"> 16 <param name="out_format1" type="select" label="Output sequence file format">
18 <label>Output Sequence File Format</label>
19 <option value="fasta">FASTA (m)</option> 17 <option value="fasta">FASTA (m)</option>
20 <option value="acedb">ACeDB (m)</option> 18 <option value="acedb">ACeDB (m)</option>
21 <option value="asn1">ASN.1 (m)</option> 19 <option value="asn1">ASN.1 (m)</option>
22 <option value="clustal">Clustal (m)</option> 20 <option value="clustal">Clustal (m)</option>
23 <option value="codata">CODATA (m)</option> 21 <option value="codata">CODATA (m)</option>
46 <option value="text">Plain sequence (s)</option> 44 <option value="text">Plain sequence (s)</option>
47 <option value="treecon">Treecon (m)</option> 45 <option value="treecon">Treecon (m)</option>
48 </param> 46 </param>
49 </inputs> 47 </inputs>
50 <outputs> 48 <outputs>
51 <data format="fasta" name="out_file1" /> 49 <data name="out_file1" format="fasta" />
52 </outputs> 50 </outputs>
53 <tests> 51 <tests>
54 <test> 52 <test>
55 <param name="input1" value="2.fasta"/> 53 <param name="input1" value="2.fasta"/>
56 <param name="regions" value="1-9999999"/> 54 <param name="regions" value="1-9999999"/>
57 <param name="separate" value="no"/> 55 <param name="separate" value="no"/>
58 <param name="out_format1" value="fasta"/> 56 <param name="out_format1" value="fasta"/>
59 <output name="out_file1" file="emboss_extractseq_out.fasta"/> 57 <output name="out_file1" file="emboss_extractseq_out.fasta"/>
60 </test> 58 </test>
61 </tests> 59 </tests>
62 <code file="emboss_format_corrector.py" />
63 <help> 60 <help>
64 You can view the original documentation here_. 61 You can view the original documentation here_.
65
66 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractseq.html
67 62
68 ------ 63 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/extractseq.html
69
70 **Citation**
71
72 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;`_
73
74 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;`_
75 </help> 64 </help>
65 <expand macro="citations" />
76 </tool> 66 </tool>