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comparison emboss_einverted.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: einverted28" name="einverted" version="5.0.0"> 1 <tool id="EMBOSS: einverted28" name="einverted" version="5.0.0.1">
2 <description>Finds DNA inverted repeats</description> 2 <description>Finds DNA inverted repeats</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>einverted -sequence '$input1' -outfile '$out_file1' -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
5 <inputs> 8 <inputs>
6 <param format="fasta" name="input1" type="data"> 9 <param name="input1" type="data" format="fasta" label="On query" />
7 <label>On query</label> 10 <param name="gap" type="integer" value="12" label="Gap penalty" />
8 </param> 11 <param name="threshold" type="integer" value="50" label="Minimum score threshold" />
9 <param name="gap" type="text" value="12"> 12 <param name="match" type="integer" value="3" label="Match score" />
10 <label>Gap penalty</label> 13 <param name="mismatch" type="integer" value="-4" label="Mismatch score" />
11 </param> 14 <param name="maxrepeat" type="integer" value="2000" label="Maximum separation between the start of repeat and the end of the inverted repeat" />
12 <param name="threshold" type="text" value="50">
13 <label>Minimum score threshold</label>
14 </param>
15 <param name="match" type="text" value="3">
16 <label>Match score</label>
17 </param>
18 <param name="mismatch" type="text" value="-4">
19 <label>Mismatch score</label>
20 </param>
21 <param name="maxrepeat" type="text" value="2000">
22 <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
23 </param>
24 </inputs> 15 </inputs>
25 <outputs> 16 <outputs>
26 <data format="einverted" name="out_file1" /> 17 <data name="out_file1" format="einverted" />
27 </outputs> 18 </outputs>
28 <tests> 19 <tests>
29 <test> 20 <test>
30 <param name="input1" value="1.fasta"/> 21 <param name="input1" value="1.fasta"/>
31 <param name="gap" value="12"/> 22 <param name="gap" value="12"/>
42 The input dataset needs to be sequences. 33 The input dataset needs to be sequences.
43 34
44 ----- 35 -----
45 36
46 You can view the original documentation here_. 37 You can view the original documentation here_.
47
48 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html
49 38
50 ------ 39 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/einverted.html
51
52 **Citation**
53
54 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;`_
55
56 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;`_
57 </help> 40 </help>
41 <expand macro="citations" />
58 </tool> 42 </tool>