view getMETAdata/getMETAdata.xml @ 39:5447fc8946ed draft default tip

Uploaded

<tool id="META" name="getMETAdata" version="1.0.0">
  <requirements>
    <requirement type="package" version="1.10.4">r-data.table</requirement>
    <requirement type="package" version="2.38.4">bioconductor-geoquery</requirement>
  </requirements>
<stdio>
   <exit_code range="1:" />
</stdio>
  <command> Rscript $__tool_directory__/getMETAdata.R "$GSMTable" "$MetaTable" </command>
 <inputs>
    <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."/>
    </param>
  </inputs>
  <outputs>
    <data format="txt" name="MetaTable" label="MetaData.txt"/>
</outputs>
  <tests>
    <test>
      <param name="test">
      <element name="test-data">
          <collection type="data">
              <element name="GSMTable" value="test-data/GSMTable.txt" />
          </collection>
        </element>
        </param>
        <output format="txt" name="MetaTable" label="test-data/MetaTable.txt"/>
        </test>
    </tests>
  <help>
**What it does**
  This R-based tool downloads data from GEO using getGEO from the GEOquery package
**Input**
 A table representing ID of GEO objects for download and parsing
**Output**
 Get a metadata table from NCBI 
</help>
<citations>
<citation type="doi">10.1093/bioinformatics/btm254</citation>
</citations>
</tool>