# HG changeset patch
# User chrisd
# Date 1456198294 18000
# Node ID b53a97d0d54c93ab7c7d2f344c48b209a29251cc

planemo upload for repository https://github.com/ChrisD11/csa_dep commit e9517a49dbeb556362b2bfafb62ca70af93106dd

diff -r 000000000000 -r b53a97d0d54c gene_fraction.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_fraction.xml	Mon Feb 22 22:31:34 2016 -0500
@@ -0,0 +1,65 @@
+<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>
+    <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" />
+	<param type="data" name="input2" format="sam" />
+	<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="1" min="1" 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[
+        
+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
+    -d         directory parsing
+    -bam       bam file parsing
+    -out_fp    output file path
+
+
+    ]]></help>
+</tool>
diff -r 000000000000 -r b53a97d0d54c test-data/ref.fa
diff -r 000000000000 -r b53a97d0d54c test-data/test.sam
diff -r 000000000000 -r b53a97d0d54c tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Feb 22 22:31:34 2016 -0500
@@ -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>