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comparison emboss_prettyseq.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: prettyseq80" name="prettyseq" version="5.0.0"> 1 <tool id="EMBOSS: prettyseq80" name="prettyseq" version="5.0.0.1">
2 <description>Output sequence with translated ranges</description> 2 <description>Output sequence with translated ranges</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>prettyseq -sequence $input1 -outfile $out_file1 -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>prettyseq -sequence '$input1' -outfile '$out_file1' -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto</command>
5 <inputs> 8 <inputs>
6 <param format="fasta" name="input1" type="data"> 9 <param name="input1" type="data" format="fasta" label="Sequence" />
7 <label>Sequence</label> 10 <param name="ruler" type="select" label="Add a ruler">
8 </param>
9 <param name="ruler" type="select">
10 <label>Add a ruler</label>
11 <option value="yes">Yes</option> 11 <option value="yes">Yes</option>
12 <option value="no">No</option> 12 <option value="no">No</option>
13 </param> 13 </param>
14 <param name="plabel" type="select"> 14 <param name="plabel" type="select" label="Number translations">
15 <label>Number translations</label>
16 <option value="yes">Yes</option> 15 <option value="yes">Yes</option>
17 <option value="no">No</option> 16 <option value="no">No</option>
18 </param> 17 </param>
19 <param name="nlabel" type="select"> 18 <param name="nlabel" type="select" label="Number DNA sequence">
20 <label>Number DNA sequence</label>
21 <option value="yes">Yes</option> 19 <option value="yes">Yes</option>
22 <option value="no">No</option> 20 <option value="no">No</option>
23 </param> 21 </param>
24 <param name="width" type="text" value="60"> 22 <param name="width" type="integer" value="60" min="10" label="Width of screen" />
25 <label>Width of screen</label>
26 </param>
27 </inputs> 23 </inputs>
28 <outputs> 24 <outputs>
29 <data format="prettyseq" name="out_file1" /> 25 <data name="out_file1" format="prettyseq" />
30 </outputs> 26 </outputs>
31 <tests> 27 <tests>
32 <test> 28 <test>
33 <param name="input1" value="2.fasta"/> 29 <param name="input1" value="2.fasta"/>
34 <param name="ruler" value="yes"/> 30 <param name="ruler" value="yes"/>
37 <param name="width" value="60"/> 33 <param name="width" value="60"/>
38 <output name="out_file1" file="emboss_prettyseq_out.prettyseq"/> 34 <output name="out_file1" file="emboss_prettyseq_out.prettyseq"/>
39 </test> 35 </test>
40 </tests> 36 </tests>
41 <help> 37 <help>
42
43 .. class:: warningmark 38 .. class:: warningmark
44 39
45 The input dataset needs to be sequences. 40 The input dataset needs to be sequences.
46 41
47 ----- 42 -----
48 43
49 You can view the original documentation here_. 44 You can view the original documentation here_.
50
51 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyseq.html
52 45
53 ------ 46 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/prettyseq.html
54
55 **Citation**
56
57 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;`_
58
59 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;`_
60 </help> 47 </help>
48 <expand macro="citations" />
61 </tool> 49 </tool>