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1 <tool id="plot_comparative" name="Visualization of comparative clustering" version="1.0.0">
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2 <description> Simple utility to create visualization of RepeatExplorer conmparative analysis</description>
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3 <requirements>
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4 <requirement type="package">r-optparse</requirement>
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5 </requirements>
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6
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7 <command interpreter="Rscript" detect_errors="exit_code" >
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8 $__tool_directory__/plot_comparative_clustering_summary.R
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9 --cluster_table=$cluster_table
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10 --comparative_counts=$counts
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11 --number_of_colors=$number_of_colors
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12 --output=$outpdf
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13 $nuclear_only
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14
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15 #if $normalization.use_genome_size:
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16 --genome_size $normalization.genome_size_table
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17 #end if
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18 </command>
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19
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20 <inputs>
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21 <param format="txt" type="data" name="cluster_table" label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv"/>
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22 <param format="txt" type="data" name="counts" label="file from RepeatExplorer2 output - COMPARATIVE_ANALYSIS_COUNTS.csv"/>
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23 <param value="10" min="2" max="20" type="integer" name="number_of_colors" label="Maximum number of color used for plottting"/>
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24 <param value="false" type="boolean" truevalue="--nuclear_only" falsevalue="" name="nuclear_only" label="Remove all non-nuclear sequences (organel and contamination)"/>
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25 <conditional name="normalization">
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26 <param name="use_genome_size" type="boolean" checked="False" label="Normalize to genome size" help="Note that if this option is used, non-nuclear sequences are always removed."/>
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27 <when value="false">
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28 <!-- pass -->
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29 </when>
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30 <when value="true">
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31 <param name="genome_size_table" type="data" format="txt" label="table with genome sizes"/>
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32
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33 </when>
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34
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35 </conditional>
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36 </inputs>
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37
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38 <outputs>
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39 <data format="pdf" name="outpdf" label="Comparative analysis summary"/>
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40 </outputs>
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41 <help>
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42 **Visualization of comparative clustering**
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43 Visualization can be created two output files from RepeatExplorer pipeline.
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44
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45 Input file CLUSTER_TABLE.csv contains automatic annotation, information about cluster sizes and the total number of reads used for analysis
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46 Example of CLUSTER_TABLE.csv: ::
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47
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48 "Number_of_reads_in_clusters" 3002
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49 "Number_of_clusters" 895
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50 "Number_of_superclusters" 895
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51 "Number_of_singlets" 6998
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52
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53 "Number_of_analyzed_reads" 10000
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54
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55 "Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation" "TAREAN_classification" "Final_annotation"
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56 1 1 61 61 "All" "Other"
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57 2 2 59 59 "All/repeat/satellite" "Putative satellites (high confidence)"
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58 3 3 45 45 "All/repeat/satellite" "Putative satellites (low confidence)"
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59 4 4 38 38 "All" "Other"
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60 5 5 32 32 "All" "Other"
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61 6 6 28 28 "All" "Other"
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62 7 7 25 25 "All" "Other"
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63 8 8 24 24 "All" "Other"
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64 9 9 23 23 "All" "Other"
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65 10 10 22 22 "All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre" "Other"
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66 11 11 20 20 "All" "Other"
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67 12 12 20 20 "All" "Other"
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68
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69
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70 </help>
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71 </tool>
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