view getMETAdata/getMETAdata.xml @ 73:63f1a36323dc draft default tip

author testtool
date Tue, 15 Aug 2017 06:08:31 -0400
parents 81b5c08c21e1
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<tool id="META" name="getMETAdata" version="1.0.0">
    <requirement type="package" version="2.38.4">bioconductor-geoquery</requirement>
   <exit_code range="1:" />
  <command> Rscript $__tool_directory__/getMETAdata.R "$GSMTable" "$MetaTable" </command>
    <param optional="false" format="txt" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable">
      <validator type="empty_field" message="This field is required."/>
    <data format="txt" name="MetaTable" label="MetaData.txt"/>
      <param name="test">
      <element name="test-data">
          <collection type="data">
              <element name="GSMTable" value="test-data/GSMTable.txt" />
        <output format="txt" name="MetaTable" label="test-data/MetaTable.txt"/>
**What it does**
  This R-based tool downloads data from GEO using getGEO from the GEOquery package
 A table representing ID of GEO objects for download and parsing
 Get a metadata table from NCBI 
<citation type="doi">10.1093/bioinformatics/btm254</citation>