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1 <tool id="kplogo" name="kpLogo" version="1.0">
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2 <description>for positional k-mer analysis</description>
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3 <command>
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4
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5 kpLogo $input $inputtype -o $output -alphabet $alphabet $maxk -startPos $startPos $degenerate 2> tmp;
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6 cp ${output}.most.significant.each.position.pdf $output;
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7 cp ${output}.pdf $logo_prob;
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8 cp ${output}.info.pdf $logo_info;
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9 cp ${output}.freq.pdf $logo_freq;
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10 cp ${output}.most.significant.each.position.txt $tab_most;
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11 cp ${output}.pass.p.cutoff.txt $tab_all;
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12
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13 </command>
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14 <inputs>
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15 <page>
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16 <param format="fasta" name="input" type="data" label="Fasta File" />
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17
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18 <param name="alphabet" type="select" label="Sequence type: DNA/RNA or Protein" >
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19 <option value="dna" selected="True">DNA/RNA</option>
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20 <option value="protein">Protein</option>
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21 <option value="other">Other (not supported yet)</option>
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22 </param>
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23
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24 <param name="inputtype" type="select" label="Weighted or Ranked" >
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25 <option value="" selected="True">Unweighted (FASTA or Tab-delimited) </option>
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26 <option value="-ranked">Ranked (FASTA or Tab-delimited)</option>
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27 <option value="-weighted">Weighted (Tab-delimited)</option>
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28 </param>
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29
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30 <param name="maxk" type="select" label="k-mer length"
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31 help="k-mer length">
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32 <option value="-max_k 4" selected="True">1,2,3,4</option>
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33 <option value="-max_k 3">1,2,3</option>
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34 <option value="-max_k 2">1,2</option>
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35 <option value="-k 4">4</option>
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36 <option value="-k 3">3</option>
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37 <option value="-k 2">2</option>
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38 <option value="-k 1">1</option>
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39 </param>
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40
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41 <param name="degenerate" type="select" label="Degenerate residual (DNA/RNA only)">
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42 <option value="-gapped" selected="True">ACGTN, i.e. gapped</option>
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43 <option value="">None (no degenerate residuals)</option>
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44 <option value="-degenerate all">all IUPAC residuals: ACGTRYMKWSBDHVN</option>
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45 </param>
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46
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47 <param name="startPos" type="integer" value="1"/>
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48
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49
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50 </page>
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51 </inputs>
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52 <outputs>
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53 <data format="pdf" name="logo_info" label="${tool.name} on ${on_string}: info"/>
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54 <data format="pdf" name="logo_freq" label="${tool.name} on ${on_string}: freq"/>
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55 <data format="pdf" name="logo_prob" label="${tool.name} on ${on_string}: prob"/>
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56 <data format="pdf" name="output" label="${tool.name} on ${on_string}: kmer"/>
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57 <data format="tabular" name="tab_all" label="${tool.name} on ${on_string}: all_kmer"/>
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58 <data format="tabular" name="tab_most" label="${tool.name} on ${on_string}: most_sig"/>
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59
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60
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61 </outputs>
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62 <help>
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63
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64 **Note**
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65
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66 This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.
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67
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68 It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed
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69 it in to this tool.
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70
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71 A typical output looks like this
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72
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73 .. image:: ${static_path}/images/rgWebLogo3_test.jpg
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74
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75 ----
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76
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77 **Warning about input Fasta format files**
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78
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79 The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. The tool will provide a warning
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80 and refuse to call the weblogo3 executable if irregular length sequences are detected.
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81
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82 Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file
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83 a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta
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84 sequences are the same length!
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85
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86 ----
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87
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88 **Attribution**
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89
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90 Weblogo attribution and associated documentation are available at Weblogo3_
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91
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92 This Galaxy wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts
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93
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94 .. _Weblogo3: http://weblogo.berkeley.edu/
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95
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96 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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97
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98 </help>
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99
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100 </tool>
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101
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102
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