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comparison emboss_dreg.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: dreg27" name="dreg" version="5.0.0"> 1 <tool id="EMBOSS: dreg27" name="dreg" version="5.0.0">
2 <description>Regular expression search of a nucleotide sequence</description> 2 <description>Regular expression search of a nucleotide sequence</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>dreg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>dreg -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto</command>
5 <inputs> 8 <inputs>
6 <param format="data" name="input1" type="data"> 9 <param name="input1" type="data" format="data" label="Sequence 1" />
7 <label>Sequence 1</label> 10 <param name="pattern" type="text" value="(AUG)" label="Regular expression pattern" />
8 </param>
9 <param name="pattern" type="text" value="(AUG)">
10 <label>Regular expression pattern</label>
11 </param>
12 </inputs> 11 </inputs>
13 <outputs> 12 <outputs>
14 <data format="dreg" name="out_file1" /> 13 <data name="out_file1" format="dreg" />
15 </outputs> 14 </outputs>
16 <!-- tests not possible since dreg timestamps output file --> 15 <!-- tests not possible since dreg timestamps output file -->
17 <help> 16 <help>
18 You can view the original documentation here_. 17 You can view the original documentation here_.
19
20 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dreg.html
21 18
22 ------ 19 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dreg.html
23
24 **Citation**
25
26 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;`_
27
28 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;`_
29 </help> 20 </help>
21 <expand macro="citations" />
30 </tool> 22 </tool>