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comparison emboss_polydot.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: polydot77" name="polydot" version="5.0.0"> 1 <tool id="EMBOSS: polydot77" name="polydot" version="5.0.0.1">
2 <!-- produces png file, not added functional tests --> 2 <!-- produces png file, not added functional tests -->
3 <description>Displays all-against-all dotplots of a set of sequences</description> 3 <description>Displays all-against-all dotplots of a set of sequences</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <macros>
5 <command interpreter="perl">emboss_single_outputfile_wrapper.pl polydot -sequence $input1 -graph png -goutfile $output2 -outfeat $output1 -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap 5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' polydot -sequence '$input1' -graph png -goutfile '$output2' -outfeat '$output1' -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap
6 $gap -auto</command> 9 $gap -auto</command>
7 <inputs> 10 <inputs>
8 <param format="fasta" name="input1" type="data"> 11 <param name="input1" type="data" format="fasta" label="Sequence" />
9 <label>Sequence</label> 12 <param name="wordsize" type="integer" value="6" label="Word size" />
10 </param> 13 <param name="boxit" type="select" label="Draw a box around each dotplot">
11 <param name="wordsize" type="text" value="6">
12 <label>Word size</label>
13 </param>
14 <param name="boxit" type="select">
15 <label>Draw a box around each dotplot</label>
16 <option value="yes">Yes</option> 14 <option value="yes">Yes</option>
17 <option value="no">No</option> 15 <option value="no">No</option>
18 </param> 16 </param>
19 <param name="gap" type="text" value="10"> 17 <param name="gap" type="integer" value="10" label="Size of gap" />
20 <label>Size of gap</label>
21 </param>
22 </inputs> 18 </inputs>
23 <outputs> 19 <outputs>
24 <data format="polydot" name="output1" /> 20 <data name="output1" format="polydot" />
25 <data format="png" name="output2" /> 21 <data name="output2" format="png" />
26 </outputs> 22 </outputs>
27 <!-- <tests> 23 <!-- <tests>
28 <test> 24 <test>
29 <param name="input1" value="2.fasta"/> 25 <param name="input1" value="2.fasta"/>
30 <param name="wordsize" value="6"/> 26 <param name="wordsize" value="6"/>
32 <param name="gap" value="10"/> 28 <param name="gap" value="10"/>
33 <output name="output1" file="emboss_polydot_out.png"/> 29 <output name="output1" file="emboss_polydot_out.png"/>
34 </test> 30 </test>
35 </tests>--> 31 </tests>-->
36 <help> 32 <help>
37
38 .. class:: warningmark 33 .. class:: warningmark
39 34
40 The input dataset needs to be sequences. 35 The input dataset needs to be sequences.
41 36
42 ----- 37 -----
43 38
44 You can view the original documentation here_. 39 You can view the original documentation here_.
45
46 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/polydot.html
47 40
48 ------ 41 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/polydot.html
49
50 **Citation**
51
52 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;`_
53
54 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;`_
55 </help> 42 </help>
43 <expand macro="citations" />
56 </tool> 44 </tool>