Mercurial > repos > devteam > emboss_5

comparison emboss_freak.xml @ 11:0e2484b6829b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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: freak36" name="freak" version="5.0.0"> 1 <tool id="EMBOSS: freak36" name="freak" version="5.0.0.1">
2 <description>Residue/base frequency table or plot</description> 2 <description>Residue/base frequency table or plot</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>freak -seqall $input1 -outfile $out_file1 -window $window -letters $letters -graph png -step $step -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>freak -seqall '$input1' -outfile '$out_file1' -window $window -letters '$letters' -graph png -step $step -auto</command>
5 <inputs> 8 <inputs>
6 <param format="data" name="input1" type="data"> 9 <param name="input1" type="data" format="data" label="Sequences" />
7 <label>Sequences</label> 10 <param name="letters" type="text" value="gc" label="Residue letters" />
8 </param> 11 <param name="step" type="integer" value="1" label="Stepping value" />
9 <param name="letters" type="text" value="gc"> 12 <param name="window" type="integer" value="30" label="Averaging window" />
10 <label>Residue letters</label>
11 </param>
12 <param name="step" type="text" value="1">
13 <label>Stepping value</label>
14 </param>
15 <param name="window" type="text" value="30">
16 <label>Averaging window</label>
17 </param>
18 </inputs> 13 </inputs>
19 <outputs> 14 <outputs>
20 <data format="freak" name="out_file1" /> 15 <data name="out_file1" format="freak" />
21 </outputs> 16 </outputs>
22 <tests> 17 <tests>
23 <test> 18 <test>
24 <param name="input1" value="2.fasta"/> 19 <param name="input1" value="2.fasta"/>
25 <param name="letters" value="gc"/> 20 <param name="letters" value="gc"/>
28 <output name="out_file1" file="emboss_freak_out.freak"/> 23 <output name="out_file1" file="emboss_freak_out.freak"/>
29 </test> 24 </test>
30 </tests> 25 </tests>
31 <help> 26 <help>
32 You can view the original documentation here_. 27 You can view the original documentation here_.
33
34 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/freak.html
35 28
36 ------ 29 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/freak.html
37
38 **Citation**
39
40 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;`_
41
42 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;`_
43 </help> 30 </help>
31 <expand macro="citations" />
44 </tool> 32 </tool>