comparison summarize_cluster_table.xml @ 19:2f1b5d5c5dd5 draft

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18:d7f3eff34c27

<tool id="summarize_annotation" name="Make summary of CLUSTER_TABLE" version="1.0.0">
  <description> Simple utility to summarize final annotation from RepeatExplorer CLUSTER_TABLE</description>
  <requirements>
    <requirement type="package">r-optparse</requirement>
  </requirements>
  
    <command interpreter="Rscript" detect_errors="exit_code" >

    <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 proportion from ${cluster_table.hid}"/>
    </outputs>
    <help>
      **Summarization of annotation from CLUSTER_TABLE**
          
      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.

      Example of CLUSTER_TABLE.csv: ::

          Number_of_reads_in_clusters	1185180					
          Number_of_clusters	62148					

19:2f1b5d5c5dd5

<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" >

    <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