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1 <tool id="mummer_tool" name="MUMmer compare and plot" version="0.4.alx" force_history_refresh="True">
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2 <description>: Compare and plot genomes (Nucmer or Promer)</description>
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3 <command interpreter="bash">
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4 mummer_tool.sh
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5 $input_ref $input_query
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6 $out_delta $out_coords $out_png $out_log
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7 $algorithm
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8 $keep_delta $make_coords $keep_log $make_image
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9 $cmd_extra
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10 </command>
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11 <inputs>
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12 <param name="algorithm" type="select" format="text" value="nucmer" label="Algorithm" help="Nucmer dna or Promer protein (FASTA: protein. Dna is six frame translated)">
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13 <option value="nucmer">Nucmer DNA</option>
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14 <option value="promer">Promer</option>
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15 </param>
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16 <param name="input_ref" type="data" format="fasta" label="Reference sequence" />
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17 <param name="input_query" type="data" format="fasta" label="Sequence query file"/>
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18 <param name="make_image" type="select" format="text" value="yes" label="Generate MUMmerplot" help="MUMmerplot will be run with default settings and --large --png as fixed image.">
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19 <option value="yes">Yes</option>
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20 <option value="no">No</option>
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21 </param>
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22 <param name="keep_delta" type="select" format="text" value="no" label="Keep delta file" help="i.e. for further processing">
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23 <option value="no">No</option>
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24 <option value="yes">Yes</option>
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25 </param>
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26 <param name="make_coords" type="select" format="text" value="yes" label="Make coords file" help="Uses the -r argument to sort lines by reference.">
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27 <option value="no">No</option>
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28 <option value="yes">Yes</option>
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29 </param>
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30 <param name="keep_log" type="select" format="text" value="no" label="Keep console log file" help="i.e. for debugging">
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31 <option value="no">No</option>
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32 <option value="yes">Yes</option>
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33 </param>
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34 <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="the --coords is run by default" />
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35 </inputs>
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36 <outputs>
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37 <data name="out_coords" format="tabular" label="${algorithm.value_label} coords">
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38 <filter>make_coords=="yes"</filter>
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39 </data>
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40 <data name="out_delta" format="tabular" label="${algorithm.value_label} delta">
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41 <filter>keep_delta=="yes"</filter>
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42 </data>
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43 <data name="out_png" format="png" label="${algorithm.value_label} mummerplot">
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44 <filter>make_image=="yes"</filter>
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45 </data>
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46 <data name="out_log" format="tabular" label="Console log file">
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47 <filter>keep_log=="yes"</filter>
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48 </data>
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49 </outputs>
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50 <requirements>
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51 <requirement type="package" version="4.6">gnuplot</requirement>
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52 <requirement type="package" version="3.23">mummer</requirement>
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53 </requirements>
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54 <tests>
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55 <test>
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56 <param name="algorithm" value="nucmer" />
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57 <param name="input_ref" value="test.seq1.fasta"/>
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58 <param name="input_query" value="test.seq2.fasta"/>
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59 <param name="make_image" value="yes"/>
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60 <param name="keep_delta" value="no" />
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61 <param name="make_coords" value="no" />
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62 <param name="keep_log" value="yes" />
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63
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64 <output name="out_log" file="test.MUMmerplot.result.Nucmer_galaxy.log" />
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65 <output name="out_png" file="test.MUMmerplot.result.Nucmer_galaxy.png" />
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66 </test>
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67 </tests>
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68 <help>
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69 |
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70
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71
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72 **Reference**
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73 -------------
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74
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75 - **Nucmer Galaxy tool wrapper: Alex Bossers, CVI of Wageningen UR, The Netherlands.**
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76
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77 - **Nucmer or Promer of MUMmer suite:** v3.22 http://mummer.sourceforge.net/manual/
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78
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79 - **MUMmer tutorials:** http://mummer.sourceforge.net/examples/
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80
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81
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82 If you found these tools/wrappers useful in your research, please acknowledge our work. If you improve
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83 or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)
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84
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85
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86 **Command line arguments**
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87 --------------------------
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88
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89 --mum Use anchor matches that are unique in both the reference and query
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90 --mumreference Use anchor matches that are unique in the reference but not necessarily unique in the query (default behavior)
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91 --maxmatch Use all anchor matches regardless of their uniqueness
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92 --breaklen Distance an alignment extension will attempt to extend poor scoring regions before giving up (default 200)
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93 --mincluster Minimum cluster length (default 65)
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94 --delta Toggle the creation of the delta file. Setting --nodelta prevents the alignment extension step and only outputs the match clusters (default --delta)
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95 --depend Print the dependency information and exit
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96 --diagfactor Maximum diagonal difference factor for clustering, i.e. diagonal difference / match separation (default 0.12)
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97 --extend Toggle the outward extension of alignments from their anchoring clusters. Setting --noextend will prevent alignment extensions but still align the DNA between clustered matches and create the .delta file (default --extend)
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98 --forward Align only the forward strands of each sequence
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99 --maxgap Maximum gap between two adjacent matches in a cluster (default 90)
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100 --help Print the help information and exit
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101 --minmatch Minimum length of an maximal exact match (default 20)
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102 --optimize Toggle alignment score optimization. Setting --nooptimize will prevent alignment score optimization and result in sometimes longer, but lower scoring alignments (default --optimize)
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103 --reverse Align only the reverse strand of the query sequence to the forward strand of the reference
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104 --simplify Simplify alignments by removing shadowed clusters. Turn this option off (--nosimplify) if aligning a sequence to itself to look for repeats (default --simplify)
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105 --version Print the version information and exit
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106 --coords **Automatically ON in galaxy wrapper!** It generates the .coords file using the 'show-coords' program with the -r option.
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107 --prefix **Do NOT use in Galaxy wrapper!** Set the output file prefix (default out)
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108
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109 |
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110 |
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111
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112 </help>
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113 </tool>
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114
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