Mercurial > repos > devteam > emboss_5
annotate emboss_5/emboss_freak.xml @ 8:b810c96613ee draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:12:41 -0500 |
parents | b94ca591877b |
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rev | line source |
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0 | 1 <tool id="EMBOSS: freak36" name="freak" version="5.0.0"> |
2 <description>Residue/base frequency table or plot</description> | |
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
4 <command>freak -seqall $input1 -outfile $out_file1 -window $window -letters $letters -graph png -step $step -auto</command> | |
5 <inputs> | |
6 <param format="data" name="input1" type="data"> | |
7 <label>Sequences</label> | |
8 </param> | |
8
b810c96613ee
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
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9 <param name="letters" type="text" value="gc"> |
0 | 10 <label>Residue letters</label> |
11 </param> | |
8
b810c96613ee
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
12 <param name="step" type="text" value="1"> |
0 | 13 <label>Stepping value</label> |
14 </param> | |
8
b810c96613ee
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
15 <param name="window" type="text" value="30"> |
0 | 16 <label>Averaging window</label> |
17 </param> | |
18 </inputs> | |
19 <outputs> | |
20 <data format="freak" name="out_file1" /> | |
21 </outputs> | |
22 <tests> | |
23 <test> | |
24 <param name="input1" value="2.fasta"/> | |
25 <param name="letters" value="gc"/> | |
26 <param name="step" value="1"/> | |
27 <param name="window" value="30"/> | |
28 <output name="out_file1" file="emboss_freak_out.freak"/> | |
29 </test> | |
30 </tests> | |
31 <help> | |
32 You can view the original documentation here_. | |
33 | |
34 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/freak.html | |
35 | |
36 ------ | |
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. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ | |
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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ | |
43 </help> | |
44 </tool> |