comparison emboss_dottup.xml @ 11:0e2484b6829b draft

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
comparison
equal deleted inserted replaced
10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: dottup26" name="dottup" version="5.0.0"> 1 <tool id="EMBOSS: dottup26" name="dottup" version="5.0.0.1">
2 <description>Displays a wordmatch dotplot of two sequences</description> 2 <description>Displays a wordmatch dotplot of two sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command interpreter="perl">emboss_single_outputfile_wrapper.pl dottup -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -boxit $boxit -graph png -xygraph png -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' dottup -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -wordsize $wordsize -boxit $boxit -graph png -xygraph png -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="input2" type="data" format="data" label="Sequence 2" />
8 </param> 11 <param name="wordsize" type="integer" value="4" label="Word size" />
9 <param format="data" name="input2" type="data"> 12 <param name="boxit" type="select" label="Draw a box around dotplot">
10 <label>Sequence 2</label>
11 </param>
12 <param name="wordsize" type="text" value="4">
13 <label>Word size</label>
14 </param>
15 <param name="boxit" type="select">
16 <label>Draw a box around dotplot</label>
17 <option value="yes">Yes</option> 13 <option value="yes">Yes</option>
18 <option value="no">No</option> 14 <option value="no">No</option>
19 </param> 15 </param>
20 </inputs> 16 </inputs>
21 <outputs> 17 <outputs>
22 <data format="png" name="out_file1" /> 18 <data name="out_file1" format="png" />
23 </outputs> 19 </outputs>
24 <!-- functional tests not possible since image output contains file name information and timestamp --> 20 <!-- functional tests not possible since image output contains file name information and timestamp -->
25 <help> 21 <help>
26 You can view the original documentation here_. 22 You can view the original documentation here_.
27
28 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dottup.html
29 23
30 ------ 24 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dottup.html
31
32 **Citation**
33
34 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;`_
35
36 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;`_
37 </help> 25 </help>
26 <expand macro="citations" />
38 </tool> 27 </tool>