<?xml version="1.0"?>
<tool id="select_compound" name="Compound Selector" version="1.0">
<description>This tool selects compounds from prediction result based on score</description>

<requirements>
        <requirement type="package" version="3.2.1">R</requirement>
</requirements>

<stdio>
	<exit_code range="1:" />
</stdio>

<command interpreter="Rscript">select_compound.R $predictionfile $LT $GT $type $SelectedCompound </command>

<inputs>
	<param name="predictionfile" type="data" format="txt,tabular,csv" label="Predition Result File" help ="upload gcac prediction result file " /> 
	<param name="type" type="select" label="Active/Positive or Inactive/Negative" help ="select type of molecule">
		<option value="Active" selected="True">Active/Positive</option> 
		<option value="Inactive">Inactive/Negative</option>
	</param> 
	<param name="GT" type="float" value="0.5" label="Score greater than and equal to" help ="define value above which compound selected default is 0.5" /> 
	<param name="LT" type="float" value="1.0" label="Score less than and equal to" help ="define value below which compound selected default is 1" /> 
</inputs>

<outputs>
	<data name="SelectedCompound" format="txt" label="Refind-${predictionfile.name}" />
</outputs>
<tests>
	<test>
		<param name="predictionfile" value="prediction_set_result.txt"  />
		<param name="type" value="Active"  />
		<param name="GT" value="0.5"  />
		<param name="LT" value="1.0"  />
		<output name="SelectedCompound" file="selected_prediction_set_result.txt" compare="sim_size" delta="4000" />
      	</test>
</tests>
<help></help>
</tool>