view survival/survival.xml @ 0:6cc0c5eb71b2 draft

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author testtool
date Fri, 29 Sep 2017 18:11:27 -0400
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<tool id="survival" name="survival" version="1.0.0">
    <description>core survival analysis</description>
    <requirements>
        <requirement type="package" version="2.40_1">r-survival</requirement>
    </requirements>
    <command detect_errors="aggressive">
        Rscript '$__tool_directory__/survival.R' '$input'  '$fit'  '$png'
    </command>
<inputs>
        <param format="csv" type="data" name="input"  value="" label="survival data" help="e.g. ''"/>
    </inputs>
    <outputs>
        <data format="csv" name="fit" label="survfit.csv" />
        <data format="png" name="png" label="survfit.png" />
    </outputs>
 <tests>
    <test>
      <param name="test">
      <element name="test-data">
          <collection type="data">
                <element format="csv" name="input" label="test-data/input.csv"/>
          </collection>
        </element>
        </param>
        <output format="csv"  name="fit" label="test-data/survfit.csv"/>
        <output fformat="png" name="png" label="test-data/survfit.png"/>
        </test>
    </tests>
  <help>
**Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier**
</help>
<citations>
 <citation>https://CRAN.R-project.org/package=survival</citation>
</citations>
</tool>