--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/transit_resampling.xml	Mon Dec 17 11:02:16 2018 -0500
@@ -0,0 +1,52 @@
+<?xml version="1.0"?>
+<tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy0">
+    <description>- determine per-gene p-values</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+    	@LINK_INPUTS@
+        #set $control_files = ','.join(['control_file_%d.wig' % idx for idx, _ in enumerate(str($controls).split(','))])
+        #for idx, filename in enumerate(str($controls).split(',')):
+            ln -s '$filename' control_file_${idx}.wig &&
+        #end for
+        transit resampling $input_files $control_files annotation.dat transit_out.txt
+        @STANDARD_OPTIONS@
+        -s $samples -n $normalization $histogram $adaptive $exclude_zero $pseudo $loess
+        ]]>
+    </command>
+    <inputs>
+        <expand macro="standard_inputs">
+            <param name="controls" type="data" format="wig" multiple="true" label="Control .wig files" />
+            <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" />
+            <param name="normalization" argument="-n" type="select" label="Normalization method">
+                <option value="TTR">TTR</option>
+            </param>
+            <param name="histogram" argument="-h" type="boolean" truevalue="-h" falsevalue="" label="Output histogram of the permutations" />
+            <param name="adaptive" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Perform adaptive resampling" />
+            <param name="exclude_zero" argument="-ez" type="boolean" truevalue="-ez" falsevalue="" label="Exclude rows with zero accross conditions" />
+            <param name="pseudo" argument="-pc" type="boolean" truevalue="-pc" falsevalue="" label="Add pseudocounts at each site" />
+            <param name="loess" argument="-l" type="boolean" truevalue="-l" falsevalue="" label="Perform LOESS Correction" help="Helps remove possible genomic position bias." />
+
+        </expand>
+    </inputs>
+    <outputs>
+        <expand macro="outputs" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" ftype="wig" value="transit-in1-rep1.wig,transit-in1-rep2.wig" />
+            <param name="controls" ftype="wig" value="transit-co1-rep1.wig,transit-co1-rep2.wig,transit-co1-rep3.wig" />
+            <param name="annotation" ftype="gff3" value="transit-in1.gff3" />
+            <param name="samples" value="1000" />
+            <param name="burnin" value="100" />
+            <output name="sites" file="resampling-sites1.txt" ftype="tabular" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+The re-sampling method is a comparative analysis the allows that can be used to determine conditional essentiality of genes. It is based on a permutation test, and is capable of determining read-counts that are significantly different across conditions.
+]]></help>
+    <expand macro="citations" />
+</tool>