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3
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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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4
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5 kpLogo $input $inputtype -o $output -alphabet $alphabet $maxk -startPos $startPos $degenerate -seq $col_seq -weight $col_weight -region $region_start,$region_end
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6 #if $background.background_model == '-bg'
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7 -bgfile $background_input
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8 #else
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9 $background.background_model
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10 #end if
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11 2> tmp;
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12 cp ${output}.most.significant.each.position.pdf $output;
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13 cp ${output}.pdf $logo_prob;
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14 cp ${output}.info.pdf $logo_info;
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15 cp ${output}.freq.pdf $logo_freq;
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16 cp ${output}.most.significant.each.position.txt $tab_most;
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17 cp ${output}.pass.p.cutoff.txt $tab_all;
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18
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19 </command>
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20 <inputs>
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21 <page>
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22 <param format="text" name="input" type="data" label="Input sequences (FASTA or Tabular)" />
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23
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24 <param name="alphabet" type="select" label="Sequence type: DNA/RNA or Protein" >
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25 <option value="dna" selected="True">DNA/RNA</option>
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26 <option value="protein">Protein</option>
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27 <option value="other">Other (not supported yet)</option>
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28 </param>
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29
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30 <param name="inputtype" type="select" label="Weighted or Ranked" >
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31 <option value="" selected="True">Unweighted (FASTA or Tab-delimited) </option>
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32 <option value="-ranked">Ranked (FASTA or Tab-delimited)</option>
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33 <option value="-weighted">Weighted (Tab-delimited)</option>
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34 </param>
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35
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36
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37 <param name="col_seq" type="integer" value="1" label="For tabular input, sequence is in this column:" />
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38
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39 <param name="col_weight" type="integer" value="2" label="For tabular input, weight is in this column:" />
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40
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41 <param name="region_start" type="integer" value="1" label="Starting from position (0 or negative numbers interpreted as distance from the end):" />
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42
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43 <param name="region_end" type="integer" value="0" label="Ending at position (0 or negative numbers interpreted as distance from the end):" />
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44
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45
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46
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47 <param name="maxk" type="select" label="k-mer length"
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48 help="k-mer length">
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49 <option value="-max_k 4" selected="True">1,2,3,4</option>
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50 <option value="-max_k 3">1,2,3</option>
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51 <option value="-max_k 2">1,2</option>
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52 <option value="-k 4">4</option>
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53 <option value="-k 3">3</option>
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54 <option value="-k 2">2</option>
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55 <option value="-k 1">1</option>
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56 </param>
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57
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58 <param name="degenerate" type="select" label="Degenerate residual (DNA/RNA only)">
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59 <option value="-gapped" selected="True">ACGTN, i.e. gapped</option>
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60 <option value="">None (no degenerate residuals)</option>
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61 <option value="-degenerate all">all IUPAC residuals: ACGTRYMKWSBDHVN</option>
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62 </param>
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63
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4
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64
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65
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66 <conditional name="background">
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67 <param name="background_model" type="select" label="Background model (only for unweighted sequences)">
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68 <option value="" selected="True">Average across all positions in input sequences</option>
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69 <option value="-shuffle 100,2">Shuffle each input sequence 100 times preserving di-residual frequency</option>
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70 <option value="-markov 1">Markov model learned from input sequences, first order</option>
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71 <option value="-bg">Background sequences (not supported yet in Galaxy)</option>
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72 </param>
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73 <when value="-bg">
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74 <param format="text" name="background_input" type="data" label="Background sequences (FASTA or Tabular)" />
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75 </when>
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76 </conditional>
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77
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78
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79
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3
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80 <param name="startPos" type="integer" value="1" label="Redefine position 1. The positions before it will be numbered as -1, -2, etc (no 0)." />
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81
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82 <param name="fix" type="float" value="0.75" label="Fixation frequency"/>
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83
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84 </page>
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85 </inputs>
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86 <outputs>
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87 <data format="pdf" name="logo_info" label="${tool.name} on ${on_string}: info"/>
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88 <data format="pdf" name="logo_freq" label="${tool.name} on ${on_string}: freq"/>
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89 <data format="pdf" name="logo_prob" label="${tool.name} on ${on_string}: prob"/>
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90 <data format="pdf" name="output" label="${tool.name} on ${on_string}: kmer"/>
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91 <data format="tabular" name="tab_all" label="${tool.name} on ${on_string}: all_kmer"/>
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92 <data format="tabular" name="tab_most" label="${tool.name} on ${on_string}: most_sig"/>
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93
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94
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95 </outputs>
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96 <help>
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97
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98 **Note**
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99
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100 This is a wrapper for the positional k-mer analysis tool kpLogo_, which is also available as a web server and stand-alone command-line tool. Please refer to the manual_ on the web server for help information.
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101
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102 To run kpLogo on local Galaxy instances, one needs to compile and install kpLogo locally. Please refer to the web server for details (click here_).
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103
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104 ----
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105
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106
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107 .. _kpLogo: http://kplogo.wi.mit.edu/
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108
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109 .. _manual: http://kplogo.wi.mit.edu/manual.html
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110
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111 .. _here: http://kplogo.wi.mit.edu/manual.html#install-kpLogo-locally
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112
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113
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114 </help>
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115
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116 </tool>
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117
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118
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