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view summarize_cluster_table.xml @ 21:f4ed6a65a2ff draft

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author petr-novak
date Thu, 27 Jul 2023 09:46:13 +0000
parents 2f1b5d5c5dd5
children 58807b35777a
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<tool id="summarize_annotation" name="Repeat proportions from CLUSTER_TABLE" version="1.0.0">
  <description> Simple utility to summarize final annotations from RepeatExplorer CLUSTER_TABLE</description>
  <requirements>
    <requirement type="package">r-optparse</requirement>
  </requirements>
  
    <command interpreter="Rscript" detect_errors="exit_code" >
    $__tool_directory__/summarize_cluster_table.R
    --cluster_table=$cluster_table
    --output=$output

    </command>

    <inputs>
      <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" />
    </inputs>

    <outputs>
         	<data format="tabular" name="output" label="Summary of repeat proportions from ${cluster_table.hid}"/>
    </outputs>
    <help>
      **The tool calculates genome proportions of identified repeats based on cluster annotations in CLUSTER_TABLE.csv**
          
	  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.

      Example of CLUSTER_TABLE.csv: ::

          Number_of_reads_in_clusters	1185180					
          Number_of_clusters	62148					
          Number_of_superclusters	62031					
          Number_of_singlets	314820					
          Number_of_analyzed_reads	1500000					
          Cluster	Supercluster	Size	Size_adjusted	Automatic_annotation	TAREAN_annotation	Final_annotation						
          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
          137	5	2094	2094	All/repeat	Other	All/repeat
          112	9	3117	3117	All/repeat/rDNA/45S_rDNA	Other	All/repeat/rDNA/45S_rDNA
          16	11	10078	10078	All/repeat/satellite	Putative satellites (high confidence)	All/repeat/satellite
          125	22	2630	2630	All/organelle/plastid	Other	All/organelle/plastid
          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

    </help>
</tool>