diff toolrfe.xml @ 5:016c69bfb2a1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolrfe.xml	Tue Jan 03 02:26:17 2017 -0500
@@ -0,0 +1,92 @@
+<tool id="featureSelectR" name="Feature Selection" >
+<description>
+ This tool used for extract best feature subsets cantaining input data for model building.   
+</description>
+<!--command interpreter="bash">step3run.sh $file1 $model $output1  2>/dev/null </command-->
+<requirements>
+        <requirement type="set_environment">FEATURE_SELECTION_R</requirement>
+                 <requirement type="set_environment">R_ROOT_DIR</requirement>
+    <requirement type="package" version="3.2.0">R</requirement>
+    <requirement type="package" version="1.0.0">caret-tools</requirement>
+</requirements>
+<command interpreter="Rscript">feature_selection.R $input $profile $finalset $function1 $resampling $repeat $number $corcutoff $SAMPLING> /dev/null 2>&amp;1 </command>
+
+<inputs>
+<param name="input"  type="data" label="Select input data file" help="input .RData file" />
+<param name="SAMPLING" type="select"  label="3(i). Select Sampling Method for imbalanced data" help="Defualt is with No sampling. you may choose downsample or upsample" >
+                <option value="garBage" selected="true">No Sampling</option>
+                <option value="downsampling">downsample</option>
+                <option value="upsampling">upsample</option>
+        </param>
+<param name="function1" type="select" display="radio" label="Select appropriate function for algorithm"  >
+                <option value="rfFuncs" selected="true">random forest based function </option>
+                <option value="lmFuncs">linear model based function</option>
+                <option value="treebagFuncs">treebag(CART) based function</option>
+                <option value="nbFuncs">neive bayes based function</option>
+</param>
+
+<param name="corcutoff"  type="float" value= "0.8" min="0.0" max = "1.0" label="Select correlation cutoff" help="values bewteen 0-1. fileds above cufoff value removed from data " />
+<param name="resampling" type="select" label="Select appropriate resampling method"  >
+                <option value="repeatedcv" selected="true">repeatedcv </option>
+                <option value="boot">boot</option>
+                <option value="cv">cv</option>
+                <option value="boot632">boot632</option>
+</param>
+ <param name="repeat" type="select" label="Set Number of times to repeat" help="default is 3 ">
+               <option value="3" selected="true">3</option>
+                <option value="1">1</option>
+                <option value="5">5</option>
+                <option value="10">10</option>
+        </param>
+<param name="number" type="select" label="Set Number of times Resample" help="default is 10">
+                <option value="10" selected="true">10</option>
+                <option value="5">5</option>
+                <option value="15">15</option>
+                <option value="20">20</option>
+                <option value="25">25</option>
+        </param>
+
+</inputs>
+<outputs>
+<data type="data" format="data" name="profile" label="$function1-profile" />
+<data type= "data" format="data" name="finalset" label="Selected_feature.RData "/>
+</outputs>
+<help>
+.. class:: infomark
+
+**RFE based feature selection for classification and regression**
+
+Input file must be  RData file obtained by converting csv file in to RData.
+
+output  "Selected_feature.RData"  file used for model building purpose.While profile
+
+represents feature selection model.
+
+Correlation cutoff value is desired for choosing independent variables For example
+
+Cutoff value = 0.8 removes all descriptors sharing equal or highet correlation values.
+
+User may choose varous resampling methods in combination with repeats and times of resample.
+
+
+
+</help>
+
+
+<tests>
+<test>
+          <param name="input" value="testinput.RData"/>
+          <param name="function1"  value="rfFuncs" />
+          <param name="corcutoff"  value="0.6" />
+          <param name="resampling"  value="repeatedcv" />
+          <param name="repeat"  value="1" />
+          <param name="number"  value="5" />
+          <param name="SAMPLING"  value="garb" />
+
+          <output name="profile" file="rfprofile.RData" compare="sim_size" delta="2000000" />
+          <output name="finalset" file="selected_fet.RData" compare="sim_size" delta="2000000"/>
+    </test>
+</tests>
+
+
+</tool>