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1 <?xml version="1.0"?>
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2 <tool id="edu.tamu.cpt.mist3" name="MIST v3" version="19.1.0.0">
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3 <description>Multiple Interrelated Sequence doT plotter.</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>cpt-macros.xml</import>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="2.7">python</requirement>
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10 <requirement type="package" version="1.76">biopython</requirement>
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11 <requirement type="package" version="8.0.192">openjdk</requirement>
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12 <requirement type="package" version="7.0.8_68">imagemagick</requirement>
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13 <requirement type="package" version="9.18">ghostscript</requirement>
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14 </requirements>
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15 <command detect_errors="aggressive">
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16 $__tool_directory__/mist3.py
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17 #set repeat_var_1 = '" "'.join([ str($var) for $var in $fasta_files ])
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18 --window "${window}"
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19 --zoom "${zoom}"
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20 --matrix "${matrix}"
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21 --files_path $output.files_path
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22 --plot_type $plot_type
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23
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24 "$repeat_var_1"
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25 > $output
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26 </command>
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27 <inputs>
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28 <param help="Sequences to plot" label="file" name="fasta_files" type="data" format="fasta" multiple="True"/>
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29
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30 <param name="plot_type" label="Plot Type" type="select">
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31 <option value="complete">[complete] Complete NxN plot</option>
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32 <option value="1vn">[1vN] 1 genome versus the rest</option>
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33 <option value="2up">[2up] Compare two genomes (see help)</option>
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34 </param>
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35
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36 <param help="How zoomed in the image is" label="zoom" name="zoom" type="integer" value="50" min="5"/>
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37
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38 <param help="Window Size" label="window" name="window" type="integer" value="10" min="5"/>
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39
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40 <param label="Comparison Matrix" name="matrix" type="select">
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41 <option value="blosum62">Blosum62</option>
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42 <option selected="True" value="edna">Extended DNA</option>
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43 <option value="ednaorig">Extended DNA (Original)</option>
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44 <option value="pam250">Pam 250</option>
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45 <option value="protidentity">Protein Identity</option>
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46 </param>
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47
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48 </inputs>
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49 <outputs>
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50 <data format="html" name="output" />
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="fasta_files" value="mist3_in.fasta"/>
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55 <param name="plot_type" value="complete"/>
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56 <param name="zoom" value="100"/>
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57 <param name="window" value="20"/>
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58 <param name="matrix" value="edna"/>
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59 <output name="output" ftype="html">
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60 <assert_contents>
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61 <has_text text="Mist Results"/>
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62 <has_text text="Each section of mist output is now clickable to view a higher resolution version of that subsection"/>
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
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67 <help>
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68 Multiple Interrlated Sequence doTplotter
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69 ========================================
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70
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71 Uses a stripped down vesion of Gepard (Dr. Jan Krumsiek/HelmholtzZentrum/IBIS) for dot plotting.
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72
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73 Plot Types
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74 ----------
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75
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76 There are three main plot types:
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77
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78 - **complete** does an N x N plot of each genome versus every other genome
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79 - **1vN** The first genome in the list is compared to each other genome
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80 - **2up** two-genome comparison
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81
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82 - If you provide TWO files and are using a protein comparison matrix, then the invidual
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83 protein sequences of both files will be compared in a "complete" style plot.
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84 - Otherwise, the first two genomes encountered will be compared.
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85
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86 Options
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87 -------
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88
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89 **Zoom**
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90
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91 Be careful with this option. It represents the number of bases to plot in
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92 a single pixel. For large genomes, this can mean very large images, and
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93 should be lowered appropriately. For a value of 50, 50 bases would be
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94 considered a single pixel in the output image. For a 1 Mbp genome comparison
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95 (say 5 x 200-kb phages), this would result in a 20,000 pixel image.
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96
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97 </help>
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98 <citations>
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99 <expand macro="citation/gepard" />
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100 <expand macro="citation/mijalisrasche" />
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101 <citation type="bibtex">
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102 @unpublished{galaxyTools,
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103 author = {A. Criscione},
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104 title = {CPT Galaxy Tools},
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105 year = {2019-2021},
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106 note = {https://github.com/tamu-cpt/galaxy-tools/}
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107 }
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108 </citation>
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109 </citations>
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110 </tool>
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