--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_fraction.xml	Wed Mar 23 17:54:53 2016 -0400
@@ -0,0 +1,63 @@
+<tool id="gene_fraction" name="Coverage Sampler" version="0.1.0">
+    <requirements>
+	<requirement type="package" version="0.1">csa</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <description>Calculates the amount of a gene that is covered from a sample of reads</description>
+    <command><![CDATA[
+	csa
+	  -amr_fp $input1
+	  -sam_fp $input2
+	  -min $min
+	  -max $max
+	  -t $threshold
+	  -skip $skip
+	  -samples $samples
+	  -out_fp $output1
+    ]]></command>
+    <inputs>
+	<param type="data" name="input1" format="fasta" label="Reference sequence" />
+	<param type="data" name="input2" format="sam" label="SAM file" />
+	<param name="min" type="integer" label="Starting sample level"
+	       value="1" min="1" max="100" help="(-min)" />
+	<param name="max" type="integer" label="Ending sample level"
+	       value="1" min="1" max="100" help="(-max)" />
+	<param name="threshold" type="integer" label="Gene threshold"
+	       value="0" min="0" max="100" help="(-t)" />
+	<param name="skip" type="integer" label="Amount of levels to skip"
+	       value="1" min="1" max="100" help="(-skip)" />
+	<param name="samples" type="integer" label="Amount of samples per level"
+	       value="1" min="1" max="100" help="(-samples)" />
+    </inputs>
+    <outputs>
+	<data name="output1" format="tabular" />
+    </outputs>
+    <tests>
+      <test>
+      <param name="input1" value="ref.fa"/>
+      <param name="input2" value="test.sam"/>
+      <output name="outfil1" file="out.txt"/>
+      </test>
+    </tests>
+    <help><![CDATA[
+This program takes iterative samples from a SAM file with the goal of identifying the amount of a gene that is covered by a sample of reads.
+        
+Program: Coverage Sampler
+
+Contact: Chris Dean <cdean11@rams.colostate.edu>
+
+Usage: csa [options]
+
+Options:
+    -amr_fp    amr database path
+    -sam_fp    sam file path
+    -min       starting level
+    -max       ending level
+    -skip      amount of levels to skip
+    -t         gene fraction threshold
+    -samples   amount of samples per level
+    -out_fp    output file path
+    ]]></help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Mar 23 17:54:53 2016 -0400
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="csa" version="0.1">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">git clone --recursive https://github.com/ChrisD11/csa.git</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>csa</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling csa requires a C++ compiler</readme>
+    </package>
+</tool_dependency>