annotate plot_comparative_clustering_summary.xml @ 27:eefed7a82001 draft

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1 <tool id="plot_comparative" name="Visualization of comparative clustering"
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2 version="1.0.0.3">
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3 <description>Simple utility to create visualization of RepeatExplorer conmparative
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4 analysis
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5 </description>
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6 <requirements>
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7 <requirement type="package">r-optparse</requirement>
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8 </requirements>
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9 <required_files>
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10 <include type="literal" path="plot_comparative_clustering_summary.R"/>
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11 </required_files>
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12 <command detect_errors="exit_code">
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13 Rscript '$__tool_directory__'/plot_comparative_clustering_summary.R
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14 --cluster_table=$cluster_table
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15 --comparative_counts=$counts
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16 --number_of_colors=$number_of_colors
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17 --output=$outpdf
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18 $nuclear_only
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19 #if $normalization.use_genome_size:
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20 --genome_size $normalization.genome_size_table
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21 #end if
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22 </command>
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24 <inputs>
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25 <param format="txt" type="data" name="cluster_table"
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26 label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv"/>
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27 <param format="txt" type="data" name="counts"
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28 label="file from RepeatExplorer2 output - COMPARATIVE_ANALYSIS_COUNTS.csv"/>
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29 <param value="10" min="2" max="20" type="integer" name="number_of_colors"
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30 label="Maximum number of color used for plottting"/>
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31 <param value="false" type="boolean" truevalue="--nuclear_only" falsevalue=""
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32 name="nuclear_only"
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33 label="Remove all non-nuclear sequences (organel and contamination)"/>
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34 <conditional name="normalization">
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35 <param name="use_genome_size" type="boolean" checked="False"
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36 label="Normalize to genome size"
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37 help="Note that if this option is used, non-nuclear sequences are always removed."/>
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38 <when value="false">
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39 <!-- pass -->
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40 </when>
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41 <when value="true">
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42 <param name="genome_size_table" type="data" format="txt"
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43 label="table with genome sizes"/>
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44
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45 </when>
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47 </conditional>
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48 </inputs>
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50 <outputs>
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51 <data format="pdf" name="outpdf" label="Comparative analysis summary"/>
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52 </outputs>
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53 <help>
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54 **Visualization of comparative clustering**
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55 Visualization can be created two output files from RepeatExplorer pipeline.
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56
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57 Input file CLUSTER_TABLE.csv contains automatic annotation, information about
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58 cluster sizes and the total number of reads used for analysis
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59 Example of CLUSTER_TABLE.csv: ::
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60
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61 "Number_of_reads_in_clusters" 3002
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62 "Number_of_clusters" 895
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63 "Number_of_superclusters" 895
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64 "Number_of_singlets" 6998
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65
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66 "Number_of_analyzed_reads" 10000
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67
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68 "Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation"
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69 "TAREAN_classification" "Final_annotation"
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70 1 1 61 61 "All" "Other"
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71 2 2 59 59 "All/repeat/satellite" "Putative satellites (high confidence)"
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72 3 3 45 45 "All/repeat/satellite" "Putative satellites (low confidence)"
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73 4 4 38 38 "All" "Other"
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74 5 5 32 32 "All" "Other"
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75 6 6 28 28 "All" "Other"
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76 7 7 25 25 "All" "Other"
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77 8 8 24 24 "All" "Other"
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78 9 9 23 23 "All" "Other"
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79 10 10 22 22
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80 "All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre"
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81 "Other"
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82 11 11 20 20 "All" "Other"
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83 12 12 20 20 "All" "Other"
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86 </help>
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87 </tool>