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comparison emboss_infoseq.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: infoseq46" name="infoseq" version="5.0.0"> 1 <tool id="EMBOSS: infoseq46" name="infoseq" version="5.0.0">
2 <!-- info contains file information always --> 2 <!-- info contains file information always -->
3 <description>Displays some simple information about sequences</description> 3 <description>Displays some simple information about sequences</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <macros>
5 <command>infoseq -sequence $input1 -outfile $out_file1 -html $html_out1 -heading $heading -usa $usa -name $disname -accession $accession -gi $gi -version $version -type $type -length $length -pgc 5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <code file="emboss_format_corrector.py" />
9 <command>infoseq -sequence '$input1' -outfile '$out_file1' -html $html_out1 -heading $heading -usa $usa -name $disname -accession $accession -gi $gi -version $version -type $type -length $length -pgc
6 $pgc -description $description -auto</command> 10 $pgc -description $description -auto</command>
7 <inputs> 11 <inputs>
8 <param format="data" name="input1" type="data"> 12 <param name="input1" type="data" format="data" label="Sequences" />
9 <label>Sequences</label> 13 <param name="html_out1" type="select" label="Format output as an HTML table">
10 </param>
11 <param name="html_out1" type="select">
12 <label>Format output as an HTML table</label>
13 <option value="no">No</option> 14 <option value="no">No</option>
14 <option value="yes">Yes</option> 15 <option value="yes">Yes</option>
15 </param> 16 </param>
16 <param name="heading" type="select"> 17 <param name="heading" type="select" label="Display column headings">
17 <label>Display column headings</label>
18 <option value="yes">Yes</option> 18 <option value="yes">Yes</option>
19 <option value="no">No</option> 19 <option value="no">No</option>
20 </param> 20 </param>
21 <param name="usa" type="select"> 21 <param name="usa" type="select" label="Display the USA of the sequence">
22 <label>Display the USA of the sequence</label>
23 <option value="yes">Yes</option> 22 <option value="yes">Yes</option>
24 <option value="no">No</option> 23 <option value="no">No</option>
25 </param> 24 </param>
26 <param name="disname" type="select"> 25 <param name="disname" type="select" label="Display 'name' column">
27 <label>Display 'name' column</label>
28 <option value="yes">Yes</option> 26 <option value="yes">Yes</option>
29 <option value="no">No</option> 27 <option value="no">No</option>
30 </param> 28 </param>
31 <param name="accession" type="select"> 29 <param name="accession" type="select" label="Display 'accession' column">
32 <label>Display 'accession' column</label>
33 <option value="yes">Yes</option> 30 <option value="yes">Yes</option>
34 <option value="no">No</option> 31 <option value="no">No</option>
35 </param> 32 </param>
36 <param name="gi" type="select"> 33 <param name="gi" type="select" label="Display 'GI' column">
37 <label>Display 'GI' column</label>
38 <option value="no">No</option> 34 <option value="no">No</option>
39 <option value="yes">Yes</option> 35 <option value="yes">Yes</option>
40 </param> 36 </param>
41 <param name="version" type="select"> 37 <param name="version" type="select" label="Display 'version' column">
42 <label>Display 'version' column</label>
43 <option value="no">No</option> 38 <option value="no">No</option>
44 <option value="yes">Yes</option> 39 <option value="yes">Yes</option>
45 </param> 40 </param>
46 <param name="type" type="select"> 41 <param name="type" type="select" label="Display 'type' column">
47 <label>Display 'type' column</label>
48 <option value="yes">Yes</option> 42 <option value="yes">Yes</option>
49 <option value="no">No</option> 43 <option value="no">No</option>
50 </param> 44 </param>
51 <param name="length" type="select"> 45 <param name="length" type="select" label="Display 'length' column">
52 <label>Display 'length' column</label>
53 <option value="yes">Yes</option> 46 <option value="yes">Yes</option>
54 <option value="no">No</option> 47 <option value="no">No</option>
55 </param> 48 </param>
56 <param name="pgc" type="select"> 49 <param name="pgc" type="select" label="Display 'percent GC content' column">
57 <label>Display 'percent GC content' column</label>
58 <option value="yes">Yes</option> 50 <option value="yes">Yes</option>
59 <option value="no">No</option> 51 <option value="no">No</option>
60 </param> 52 </param>
61 <param name="description" type="select"> 53 <param name="description" type="select" label="Display 'description' column">
62 <label>Display 'description' column</label>
63 <option value="yes">Yes</option> 54 <option value="yes">Yes</option>
64 <option value="no">No</option> 55 <option value="no">No</option>
65 </param> 56 </param>
66 </inputs> 57 </inputs>
67 <outputs> 58 <outputs>
68 <data format="txt" name="out_file1" /> 59 <data name="out_file1" format="txt" />
69 </outputs> 60 </outputs>
70 <code file="emboss_format_corrector.py" />
71 <help> 61 <help>
72 You can view the original documentation here_. 62 You can view the original documentation here_.
73
74 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/infoseq.html
75 63
76 ------ 64 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/infoseq.html
77
78 **Citation**
79
80 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;`_
81
82 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;`_
83 </help> 65 </help>
66 <expand macro="citations" />
84 </tool> 67 </tool>