<?xml version="1.0"?>
<tool id="candidate_compound_selector" name="Candidate Compound Selector" version="1.0">

	<description>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>