comparison summarize_cluster_table.xml @ 18:d7f3eff34c27 draft

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author petr-novak
date Fri, 14 May 2021 11:08:46 +0000
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17:d14b68e9fd1d 18:d7f3eff34c27
1 <tool id="summarize_annotation" name="Make summary of CLUSTER_TABLE" version="1.0.0">
2 <description> Simple utility to summarize final annotation from RepeatExplorer CLUSTER_TABLE</description>
3 <requirements>
4 <requirement type="package">r-optparse</requirement>
5 </requirements>
6
7 <command interpreter="Rscript" detect_errors="exit_code" >
8 $__tool_directory__/summarize_cluster_table.R
9 --cluster_table=$cluster_table
10 --output=$output
11
12 </command>
13
14 <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" />
16 </inputs>
17
18 <outputs>
19 <data format="tabular" name="output" label="Summary of repeat proportion from ${cluster_table.hid}"/>
20 </outputs>
21 <help>
22 **Summarization of annotation from CLUSTER_TABLE**
23
24 Input file CLUSTER_TABLE.csv must contains filled "Final_annotation" column. Contamination and organelle clusters are discarded from quantification, cluster table must also contain header - see example.
25
26 Example of CLUSTER_TABLE.csv: ::
27
28 Number_of_reads_in_clusters 1185180
29 Number_of_clusters 62148
30 Number_of_superclusters 62031
31 Number_of_singlets 314820
32 Number_of_analyzed_reads 1500000
33 Cluster Supercluster Size Size_adjusted Automatic_annotation TAREAN_annotation Final_annotation
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
35 137 5 2094 2094 All/repeat Other All/repeat
36 112 9 3117 3117 All/repeat/rDNA/45S_rDNA Other All/repeat/rDNA/45S_rDNA
37 16 11 10078 10078 All/repeat/satellite Putative satellites (high confidence) All/repeat/satellite
38 125 22 2630 2630 All/organelle/plastid Other All/organelle/plastid
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
40
41 </help>
42 </tool>