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comparison plot_comparative_clustering_summary.xml @ 22:58807b35777a draft

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planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author petr-novak
date Wed, 02 Aug 2023 11:31:12 +0000
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comparison
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21:f4ed6a65a2ff 22:58807b35777a
1 <tool id="plot_comparative" name="Visualization of comparative clustering" version="1.0.0"> 1 <tool id="plot_comparative" name="Visualization of comparative clustering"
2 <description> Simple utility to create visualization of RepeatExplorer conmparative analysis</description> 2 version="1.0.0.3">
3 <requirements> 3 <description>Simple utility to create visualization of RepeatExplorer conmparative
4 <requirement type="package">r-optparse</requirement> 4 analysis
5 </requirements> 5 </description>
6 6 <requirements>
7 <command interpreter="Rscript" detect_errors="exit_code" > 7 <requirement type="package">r-optparse</requirement>
8 $__tool_directory__/plot_comparative_clustering_summary.R 8 </requirements>
9 --cluster_table=$cluster_table 9 <required_files>
10 --comparative_counts=$counts 10 <include type="literal" path="plot_comparative_clustering_summary.R"/>
11 --number_of_colors=$number_of_colors 11 </required_files>
12 --output=$outpdf 12 <command detect_errors="exit_code">
13 $nuclear_only 13 Rscript '$__tool_directory__'/plot_comparative_clustering_summary.R
14 14 --cluster_table=$cluster_table
15 #if $normalization.use_genome_size: 15 --comparative_counts=$counts
16 --genome_size $normalization.genome_size_table 16 --number_of_colors=$number_of_colors
17 #end if 17 --output=$outpdf
18 $nuclear_only
19 #if $normalization.use_genome_size:
20 --genome_size $normalization.genome_size_table
21 #end if
18 </command> 22 </command>
19 23
20 <inputs> 24 <inputs>
21 <param format="txt" type="data" name="cluster_table" label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv"/> 25 <param format="txt" type="data" name="cluster_table"
22 <param format="txt" type="data" name="counts" label="file from RepeatExplorer2 output - COMPARATIVE_ANALYSIS_COUNTS.csv"/> 26 label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv"/>
23 <param value="10" min="2" max="20" type="integer" name="number_of_colors" label="Maximum number of color used for plottting"/> 27 <param format="txt" type="data" name="counts"
24 <param value="false" type="boolean" truevalue="--nuclear_only" falsevalue="" name="nuclear_only" label="Remove all non-nuclear sequences (organel and contamination)"/> 28 label="file from RepeatExplorer2 output - COMPARATIVE_ANALYSIS_COUNTS.csv"/>
25 <conditional name="normalization"> 29 <param value="10" min="2" max="20" type="integer" name="number_of_colors"
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."/> 30 label="Maximum number of color used for plottting"/>
27 <when value="false"> 31 <param value="false" type="boolean" truevalue="--nuclear_only" falsevalue=""
28 <!-- pass --> 32 name="nuclear_only"
29 </when> 33 label="Remove all non-nuclear sequences (organel and contamination)"/>
30 <when value="true"> 34 <conditional name="normalization">
31 <param name="genome_size_table" type="data" format="txt" label="table with genome sizes"/> 35 <param name="use_genome_size" type="boolean" checked="False"
36 label="Normalize to genome size"
37 help="Note that if this option is used, non-nuclear sequences are always removed."/>
38 <when value="false">
39 <!-- pass -->
40 </when>
41 <when value="true">
42 <param name="genome_size_table" type="data" format="txt"
43 label="table with genome sizes"/>
32 44
33 </when> 45 </when>
34 46
35 </conditional> 47 </conditional>
36 </inputs> 48 </inputs>
37 49
38 <outputs> 50 <outputs>
39 <data format="pdf" name="outpdf" label="Comparative analysis summary"/> 51 <data format="pdf" name="outpdf" label="Comparative analysis summary"/>
40 </outputs> 52 </outputs>
41 <help> 53 <help>
42 **Visualization of comparative clustering** 54 **Visualization of comparative clustering**
43 Visualization can be created two output files from RepeatExplorer pipeline. 55 Visualization can be created two output files from RepeatExplorer pipeline.
44
45 Input file CLUSTER_TABLE.csv contains automatic annotation, information about cluster sizes and the total number of reads used for analysis
46 Example of CLUSTER_TABLE.csv: ::
47 56
48 "Number_of_reads_in_clusters" 3002 57 Input file CLUSTER_TABLE.csv contains automatic annotation, information about
49 "Number_of_clusters" 895 58 cluster sizes and the total number of reads used for analysis
50 "Number_of_superclusters" 895 59 Example of CLUSTER_TABLE.csv: ::
51 "Number_of_singlets" 6998
52 60
53 "Number_of_analyzed_reads" 10000 61 "Number_of_reads_in_clusters" 3002
54 62 "Number_of_clusters" 895
55 "Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation" "TAREAN_classification" "Final_annotation" 63 "Number_of_superclusters" 895
56 1 1 61 61 "All" "Other" 64 "Number_of_singlets" 6998
57 2 2 59 59 "All/repeat/satellite" "Putative satellites (high confidence)" 65
58 3 3 45 45 "All/repeat/satellite" "Putative satellites (low confidence)" 66 "Number_of_analyzed_reads" 10000
59 4 4 38 38 "All" "Other" 67
60 5 5 32 32 "All" "Other" 68 "Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation"
61 6 6 28 28 "All" "Other" 69 "TAREAN_classification" "Final_annotation"
62 7 7 25 25 "All" "Other" 70 1 1 61 61 "All" "Other"
63 8 8 24 24 "All" "Other" 71 2 2 59 59 "All/repeat/satellite" "Putative satellites (high confidence)"
64 9 9 23 23 "All" "Other" 72 3 3 45 45 "All/repeat/satellite" "Putative satellites (low confidence)"
65 10 10 22 22 "All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre" "Other" 73 4 4 38 38 "All" "Other"
66 11 11 20 20 "All" "Other" 74 5 5 32 32 "All" "Other"
67 12 12 20 20 "All" "Other" 75 6 6 28 28 "All" "Other"
76 7 7 25 25 "All" "Other"
77 8 8 24 24 "All" "Other"
78 9 9 23 23 "All" "Other"
79 10 10 22 22
80 "All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre"
81 "Other"
82 11 11 20 20 "All" "Other"
83 12 12 20 20 "All" "Other"
68 84
69 85
70 </help> 86 </help>
71 </tool> 87 </tool>