--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/consol_fit.xml	Fri Aug 12 16:44:38 2016 -0400
@@ -0,0 +1,81 @@
+<tool id="consolidate_fitnesses" name="Consolidate Fitnesses">
+  <description>of transposon insertion locations</description>
+  <requirements>
+    <requirement type="package" version="1.64">biopython</requirement>
+  </requirements>
+  <command interpreter="python">
+    consol_fit.py  
+    -i $input 
+    -calctxt $calctxt
+    -out $output 
+    -out2 $output2 
+    -maxweight $maxweight
+    -cutoff $cutoff
+    -cutoff2 $cutoff2
+    -wig $output3
+    #if $normalization.calculations  == "yes":
+      -normalize $normalization.genes
+    #end if
+    #if $multiply.choice  == "yes":
+      -multiply $multiply.factor
+    #end if
+    #if $reads.downstream  == "yes":
+      -d 1
+    #end if
+  </command>
+  <inputs>
+    <param name="input" type="data" label="Fitness file"/>
+    <param name="calctxt" type="data" label="the txt file output from calc_fitness"/>
+    <conditional name="normalization">
+      <param name="calculations" type="select" label="Normalize fitness calculations?">
+        <option value="no">No</option>
+        <option value="yes">Yes</option>
+      </param>
+      <when value="no">
+        <!-- do nothing -->
+      </when>
+      <when value="yes"> 
+        <param name="genes" type="data" label="Genes to normalize by" />
+      </when>
+    </conditional>
+    <param name="cutoff" type="float" value="0.0" label="Cutoff"/>
+    <param name="cutoff2" type="float" value="0.0" label="Cutoff2"/>
+    <param name="maxweight" type="float" value="75" label="Maximum weight of a transposon gene in normalization calculations"/>
+    <conditional name="multiply">
+      <param name="choice" type="select" label="Multiply fitness scores by a certain value?">
+        <option value="no">No</option>
+        <option value="yes">Yes</option>
+      </param>
+      <when value="no">
+        <!-- do nothing -->
+      </when>
+      <when value="yes"> 
+        <param name="factor" type="float" value="0.0" label="Multiply by" />
+      </when>
+    </conditional>
+    <conditional name="reads">
+      <param name="downstream" type="select" label="Are all reads downstream of the transposon?">
+        <option value="no">No</option>
+        <option value="yes">Yes</option>
+      </param>
+      <when value="no">
+        <!-- do nothing -->
+      </when>
+      <when value="yes"> 
+        <!-- do nothing -->
+      </when>
+    </conditional>
+  </inputs>
+    <outputs>
+        <data format="csv" name="output" />
+        <data format="txt" name="output2" />
+        <data format="wig" name="output3" />
+    </outputs>
+  <help>
+
+**What it does**
+
+This tool consolidates the fitness values of transposon insertion mutations generated by Tn-Seq, and is mostly useful for consolidating values produced by a 4-cycle looping trimming pipeline.
+
+</help>
+</tool>
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