Mercurial > repos > devteam > emboss_5
comparison emboss_dan.xml @ 10:9b98d3d903c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
| author | devteam |
|---|---|
| date | Fri, 12 Aug 2016 19:17:10 -0400 |
| parents | |
| children | 0e2484b6829b |
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| 9:18a63c800a4d | 10:9b98d3d903c6 |
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| 1 <tool id="EMBOSS: dan19" name="dan" version="5.0.0"> | |
| 2 <description>Calculates DNA RNA/DNA melting temperature</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc | |
| 5 -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command> | |
| 6 <inputs> | |
| 7 <param format="data" name="input1" type="data"> | |
| 8 <label>On query</label> | |
| 9 </param> | |
| 10 <param name="window" type="text" value="20"> | |
| 11 <label>Window Size</label> | |
| 12 </param> | |
| 13 <param name="shift" type="text" value="1"> | |
| 14 <label>Step size (shift increment)</label> | |
| 15 </param> | |
| 16 <param name="dnaconc" type="text" value="50.0"> | |
| 17 <label>DNA Concentration (nM)</label> | |
| 18 </param> | |
| 19 <param name="saltconc" type="text" value="50.0"> | |
| 20 <label>Salt concentration (mM)</label> | |
| 21 </param> | |
| 22 <param name="thermo" type="select"> | |
| 23 <label>Output the DeltaG, DeltaH and DeltaS values</label> | |
| 24 <option value="yes">Yes</option> | |
| 25 <option value="no">No</option> | |
| 26 </param> | |
| 27 <param name="temperature" type="text" value="25 "> | |
| 28 <label>Temperature at which to calculate the DeltaG, DeltaH and DeltaS values</label> | |
| 29 </param> | |
| 30 <param name="rna" type="select"> | |
| 31 <label>Sequence is RNA</label> | |
| 32 <option value="no">No</option> | |
| 33 <option value="yes">Yes</option> | |
| 34 </param> | |
| 35 <param name="product" type="select"> | |
| 36 <label>Include percent formamide, percent of mismatches allowed and product length</label> | |
| 37 <option value="no">No</option> | |
| 38 <option value="yes">Yes</option> | |
| 39 </param> | |
| 40 <param name="formamide" type="text" value="0 "> | |
| 41 <label>Formamide concentration (nM)</label> | |
| 42 </param> | |
| 43 <param name="mismatch" type="text" value="0 "> | |
| 44 <label>Percent mismatch to be used in calculations</label> | |
| 45 </param> | |
| 46 <param name="prodlen" type="text" value="20"> | |
| 47 <label>Product length to be used in calculations</label> | |
| 48 </param> | |
| 49 <param name="plot1" type="select"> | |
| 50 <label>Create a graph</label> | |
| 51 <option value="no">No</option> | |
| 52 <option value="yes">Yes</option> | |
| 53 </param> | |
| 54 </inputs> | |
| 55 <outputs> | |
| 56 <data format="dan" name="out_file1" /> | |
| 57 </outputs> | |
| 58 <!-- | |
| 59 <tests> | |
| 60 <test> | |
| 61 <param name="input1" value="2.fasta"/> | |
| 62 <param name="window" value="20"/> | |
| 63 <param name="shift" value="1"/> | |
| 64 <param name="dnaconc" value="50"/> | |
| 65 <param name="saltconc" value="50"/> | |
| 66 <param name="thermo" value="yes"/> | |
| 67 <param name="temperature" value="25"/> | |
| 68 <param name="rna" value="no"/> | |
| 69 <param name="product" value="no"/> | |
| 70 <param name="formamide" value="0"/> | |
| 71 <param name="mismatch" value="0"/> | |
| 72 <param name="prodlen" value="20"/> | |
| 73 <param name="plot1" value="yes"/> | |
| 74 <output name="out_file1" file="emboss_dan_out.png"/> | |
| 75 </test> | |
| 76 </tests> | |
| 77 --> | |
| 78 <code file="emboss_format_corrector.py" /> | |
| 79 <help> | |
| 80 You can view the original documentation here_. | |
| 81 | |
| 82 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html | |
| 83 | |
| 84 ------ | |
| 85 | |
| 86 **Citation** | |
| 87 | |
| 88 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>`_ | |
| 89 | |
| 90 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>`_ | |
| 91 </help> | |
| 92 </tool> |