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comparison emboss_textsearch.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: textsearch98" name="textsearch" version="5.0.0"> 1 <tool id="EMBOSS: textsearch98" name="textsearch" version="5.0.0">
2 <description>Search sequence documentation. Slow, use SRS and Entrez!</description> 2 <description>Search sequence documentation. Slow, use SRS and Entrez!</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>textsearch -sequence $input1 -outfile $out_file1 -pattern "$pattern" -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>textsearch -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html
5 $html_out1 -auto</command> 9 $html_out1 -auto</command>
6 <inputs> 10 <inputs>
7 <param format="data" name="input1" type="data"> 11 <param name="input1" type="data" format="data" label="Sequence" />
8 <label>Sequence</label> 12 <param name="pattern" type="text" value="" label="Pattern to search for" />
9 </param> 13 <param name="casesensitive" type="select" label="Do a case-sensitive search">
10 <param name="pattern" type="text" value="">
11 <label>Pattern to search for</label>
12 </param>
13 <param name="casesensitive" type="select">
14 <label>Do a case-sensitive search</label>
15 <option value="no">No</option> 14 <option value="no">No</option>
16 <option value="yes">Yes</option> 15 <option value="yes">Yes</option>
17 </param> 16 </param>
18 <param name="heading" type="select"> 17 <param name="heading" type="select" label="Display column headings">
19 <label>Display column headings</label>
20 <option value="yes">Yes</option> 18 <option value="yes">Yes</option>
21 <option value="no">No</option> 19 <option value="no">No</option>
22 </param> 20 </param>
23 <param name="usa" type="select"> 21 <param name="usa" type="select" label="Display the USA of the sequence">
24 <label>Display the USA of the sequence</label>
25 <option value="yes">Yes</option> 22 <option value="yes">Yes</option>
26 <option value="no">No</option> 23 <option value="no">No</option>
27 </param> 24 </param>
28 <param name="accession" type="select"> 25 <param name="accession" type="select" label="Display accession column">
29 <label>Display accession column</label>
30 <option value="yes">Yes</option> 26 <option value="yes">Yes</option>
31 <option value="no">No</option> 27 <option value="no">No</option>
32 </param> 28 </param>
33 <param name="search_name" type="select"> 29 <param name="search_name" type="select" label="Display name column">
34 <label>Display name column</label>
35 <option value="yes">Yes</option> 30 <option value="yes">Yes</option>
36 <option value="no">No</option> 31 <option value="no">No</option>
37 </param> 32 </param>
38 <param name="description" type="select"> 33 <param name="description" type="select" label="Display description column">
39 <label>Display description column</label>
40 <option value="yes">Yes</option> 34 <option value="yes">Yes</option>
41 <option value="no">No</option> 35 <option value="no">No</option>
42 </param> 36 </param>
43 <param name="html_out1" type="select"> 37 <param name="html_out1" type="select" label="Format output as an HTML table">
44 <label>Format output as an HTML table</label>
45 <option value="no">No</option> 38 <option value="no">No</option>
46 <option value="yes">Yes</option> 39 <option value="yes">Yes</option>
47 </param> 40 </param>
48 </inputs> 41 </inputs>
49 <outputs> 42 <outputs>
50 <data format="textsearch" name="out_file1" /> 43 <data name="out_file1" format="textsearch" />
51 </outputs> 44 </outputs>
52 <code file="emboss_format_corrector.py" />
53 <help> 45 <help>
54 You can view the original documentation here_. 46 You can view the original documentation here_.
55
56 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/textsearch.html
57 47
58 ------ 48 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/textsearch.html
59
60 **Citation**
61
62 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;`_
63
64 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;`_
65 </help> 49 </help>
50 <expand macro="citations" />
66 </tool> 51 </tool>