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comparison summarize_cluster_table.xml @ 19:2f1b5d5c5dd5 draft

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author petr-novak
date Tue, 18 May 2021 11:03:57 +0000
parents d7f3eff34c27
children 58807b35777a
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18:d7f3eff34c27 19:2f1b5d5c5dd5
1 <tool id="summarize_annotation" name="Make summary of CLUSTER_TABLE" version="1.0.0"> 1 <tool id="summarize_annotation" name="Repeat proportions from CLUSTER_TABLE" version="1.0.0">
2 <description> Simple utility to summarize final annotation from RepeatExplorer CLUSTER_TABLE</description> 2 <description> Simple utility to summarize final annotations from RepeatExplorer CLUSTER_TABLE</description>
3 <requirements> 3 <requirements>
4 <requirement type="package">r-optparse</requirement> 4 <requirement type="package">r-optparse</requirement>
5 </requirements> 5 </requirements>
6 6
7 <command interpreter="Rscript" detect_errors="exit_code" > 7 <command interpreter="Rscript" detect_errors="exit_code" >
14 <inputs> 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" /> 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> 16 </inputs>
17 17
18 <outputs> 18 <outputs>
19 <data format="tabular" name="output" label="Summary of repeat proportion from ${cluster_table.hid}"/> 19 <data format="tabular" name="output" label="Summary of repeat proportions from ${cluster_table.hid}"/>
20 </outputs> 20 </outputs>
21 <help> 21 <help>
22 **Summarization of annotation from CLUSTER_TABLE** 22 **The tool calculates genome proportions of identified repeats based on cluster annotations in CLUSTER_TABLE.csv**
23 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. 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 25
26 Example of CLUSTER_TABLE.csv: :: 26 Example of CLUSTER_TABLE.csv: ::
27 27
28 Number_of_reads_in_clusters 1185180 28 Number_of_reads_in_clusters 1185180
29 Number_of_clusters 62148 29 Number_of_clusters 62148