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comparison summarize_cluster_table.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
parents 2f1b5d5c5dd5
children 628b235d76c7
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21:f4ed6a65a2ff 22:58807b35777a
1 <tool id="summarize_annotation" name="Repeat proportions from CLUSTER_TABLE" version="1.0.0"> 1 <tool id="summarize_annotation" name="Repeat proportions from CLUSTER_TABLE"
2 <description> Simple utility to summarize final annotations from RepeatExplorer CLUSTER_TABLE</description> 2 version="1.0.0.3">
3 <requirements> 3 <description>Simple utility to summarize final annotations from RepeatExplorer
4 <requirement type="package">r-optparse</requirement> 4 CLUSTER_TABLE
5 </requirements> 5 </description>
6 6 <requirements>
7 <command interpreter="Rscript" detect_errors="exit_code" > 7 <requirement type="package">r-optparse</requirement>
8 $__tool_directory__/summarize_cluster_table.R 8 </requirements>
9 --cluster_table=$cluster_table 9 <required_files>
10 --output=$output 10 <include type="literal" path="summarize_cluster_table.R"/>
11 </required_files>
12 <command interpreter="Rscript" detect_errors="exit_code">
13 Rscript $__tool_directory__/summarize_cluster_table.R
14 --cluster_table=$cluster_table
15 --output=$output
11 16
12 </command> 17 </command>
13 18
14 <inputs> 19 <inputs>
15 <param format="txt" type="data" name="cluster_table" label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv" help="CLUSTER_TABLE.csv must contains completed Final_annotation column" /> 20 <param format="txt" type="data" name="cluster_table"
21 label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv"
22 help="CLUSTER_TABLE.csv must contains completed Final_annotation column"/>
16 </inputs> 23 </inputs>
17 24
18 <outputs> 25 <outputs>
19 <data format="tabular" name="output" label="Summary of repeat proportions from ${cluster_table.hid}"/> 26 <data format="tabular" name="output"
27 label="Summary of repeat proportions from ${cluster_table.hid}"/>
20 </outputs> 28 </outputs>
21 <help> 29 <help>
22 **The tool calculates genome proportions of identified repeats based on cluster annotations in CLUSTER_TABLE.csv** 30 **The tool calculates genome proportions of identified repeats based on cluster
23 31 annotations in CLUSTER_TABLE.csv**
24 The column "Final_annotation" must be filled in the input file CLUSTER_TABLE.csv. Contamination and organelle clusters are discarded from quantification. Table header with information about numbers of analyzed reads should remain unchanged - see example below.
25 32
26 Example of CLUSTER_TABLE.csv: :: 33 The column "Final_annotation" must be filled in the input file CLUSTER_TABLE.csv.
34 Contamination and organelle clusters are discarded from quantification. Table
35 header with information about numbers of analyzed reads should remain unchanged -
36 see example below.
27 37
28 Number_of_reads_in_clusters 1185180 38 Example of CLUSTER_TABLE.csv: ::
29 Number_of_clusters 62148 39
30 Number_of_superclusters 62031 40 Number_of_reads_in_clusters 1185180
31 Number_of_singlets 314820 41 Number_of_clusters 62148
32 Number_of_analyzed_reads 1500000 42 Number_of_superclusters 62031
33 Cluster Supercluster Size Size_adjusted Automatic_annotation TAREAN_annotation Final_annotation 43 Number_of_singlets 314820
34 10 4 11967 11967 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE Other All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE 44 Number_of_analyzed_reads 1500000
35 137 5 2094 2094 All/repeat Other All/repeat 45 Cluster Supercluster Size Size_adjusted Automatic_annotation TAREAN_annotation
36 112 9 3117 3117 All/repeat/rDNA/45S_rDNA Other All/repeat/rDNA/45S_rDNA 46 Final_annotation
37 16 11 10078 10078 All/repeat/satellite Putative satellites (high confidence) All/repeat/satellite 47 10 4 11967 11967 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE Other
38 125 22 2630 2630 All/organelle/plastid Other All/organelle/plastid 48 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE
39 124 40 2645 2645 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana Putative LTR elements All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana 49 137 5 2094 2094 All/repeat Other All/repeat
50 112 9 3117 3117 All/repeat/rDNA/45S_rDNA Other All/repeat/rDNA/45S_rDNA
51 16 11 10078 10078 All/repeat/satellite Putative satellites (high confidence)
52 All/repeat/satellite
53 125 22 2630 2630 All/organelle/plastid Other All/organelle/plastid
54 124 40 2645 2645 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana Putative
55 LTR elements All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana
40 56
41 </help> 57 </help>
42 </tool> 58 </tool>