# HG changeset patch
# User anmoljh
# Date 1497272392 14400
# Node ID 557baa97ed72ef2d58bd9be2bb858b0c03dd6916

planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty

diff -r 000000000000 -r 557baa97ed72 select_compound.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/select_compound.R	Mon Jun 12 08:59:52 2017 -0400
@@ -0,0 +1,19 @@
+args <- commandArgs(T)
+arg1 <- args[1] ## Reae Input prediction file
+arg2 <- args[2] ## Less Than  
+arg3 <- args[3] ## Greater Than or equal too
+arg4 <- args[4] ## Active / Inactive
+arg5 <- args[5] ## define output file name
+asd <- read.table(arg1,row.names=1,header=T)
+if (arg4 == "Active") {
+refined <- asd[asd[,1] >= as.numeric(arg3) & asd[,1] <= as.numeric(arg2),] 
+compound  <- rownames(refined)
+refined <- cbind(compound,refined)
+} else if((arg4 == "Inactive") ){
+#refined <- asd[asd[,1] <= as.numeric(arg2),] 
+refined <- asd[asd[,2] >= as.numeric(arg3) & asd[,2] <= as.numeric(arg2),]
+compound  <- rownames(refined)
+refined <- cbind(compound,refined)}
+###write.table(dw,file=args3,row.names=FALSE,sep="\t")
+write.table(refined,file=arg5,row.names=FALSE,sep="\t")
+
diff -r 000000000000 -r 557baa97ed72 select_compound.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/select_compound.xml	Mon Jun 12 08:59:52 2017 -0400
@@ -0,0 +1,34 @@
+<?xml version="1.0"?>
+<tool id="select_compound" name="Select Compounds based of score" version="1.0">
+<description>This tool selects compounds from prediction result based on given score</description>
+
+<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>