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annotate emboss_dan.xml @ 10:9b98d3d903c6 draft

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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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10
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1 <tool id="EMBOSS: dan19" name="dan" version="5.0.0">
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2 <description>Calculates DNA RNA/DNA melting temperature</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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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
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5 -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
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6 <inputs>
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7 <param format="data" name="input1" type="data">
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8 <label>On query</label>
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9 </param>
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10 <param name="window" type="text" value="20">
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11 <label>Window Size</label>
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12 </param>
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13 <param name="shift" type="text" value="1">
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14 <label>Step size (shift increment)</label>
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15 </param>
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16 <param name="dnaconc" type="text" value="50.0">
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17 <label>DNA Concentration (nM)</label>
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18 </param>
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19 <param name="saltconc" type="text" value="50.0">
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20 <label>Salt concentration (mM)</label>
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21 </param>
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22 <param name="thermo" type="select">
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23 <label>Output the DeltaG, DeltaH and DeltaS values</label>
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24 <option value="yes">Yes</option>
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25 <option value="no">No</option>
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26 </param>
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27 <param name="temperature" type="text" value="25 ">
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28 <label>Temperature at which to calculate the DeltaG, DeltaH and DeltaS values</label>
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29 </param>
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30 <param name="rna" type="select">
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31 <label>Sequence is RNA</label>
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32 <option value="no">No</option>
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33 <option value="yes">Yes</option>
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34 </param>
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35 <param name="product" type="select">
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36 <label>Include percent formamide, percent of mismatches allowed and product length</label>
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37 <option value="no">No</option>
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38 <option value="yes">Yes</option>
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39 </param>
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40 <param name="formamide" type="text" value="0 ">
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41 <label>Formamide concentration (nM)</label>
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42 </param>
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43 <param name="mismatch" type="text" value="0 ">
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44 <label>Percent mismatch to be used in calculations</label>
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45 </param>
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46 <param name="prodlen" type="text" value="20">
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47 <label>Product length to be used in calculations</label>
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48 </param>
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49 <param name="plot1" type="select">
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50 <label>Create a graph</label>
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51 <option value="no">No</option>
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52 <option value="yes">Yes</option>
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53 </param>
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54 </inputs>
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55 <outputs>
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56 <data format="dan" name="out_file1" />
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57 </outputs>
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58 <!--
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59 <tests>
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60 <test>
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61 <param name="input1" value="2.fasta"/>
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62 <param name="window" value="20"/>
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63 <param name="shift" value="1"/>
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64 <param name="dnaconc" value="50"/>
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65 <param name="saltconc" value="50"/>
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66 <param name="thermo" value="yes"/>
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67 <param name="temperature" value="25"/>
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68 <param name="rna" value="no"/>
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69 <param name="product" value="no"/>
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70 <param name="formamide" value="0"/>
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71 <param name="mismatch" value="0"/>
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72 <param name="prodlen" value="20"/>
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73 <param name="plot1" value="yes"/>
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74 <output name="out_file1" file="emboss_dan_out.png"/>
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75 </test>
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76 </tests>
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77 -->
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78 <code file="emboss_format_corrector.py" />
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79 <help>
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80 You can view the original documentation here_.
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81
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82 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html
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83
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84 ------
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85
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86 **Citation**
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87
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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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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89
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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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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91 </help>
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92 </tool>