# HG changeset patch
# User chrisd
# Date 1456188205 18000
# Node ID 4b10ed36eb916a1621ef616df2532bc9533f98ab

planemo upload for repository https://github.com/ChrisD11/snp_caller_dep commit 6abdb1a7169f828f14104fece8a69a81e92717f4

diff -r 000000000000 -r 4b10ed36eb91 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Feb 22 19:43:25 2016 -0500
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="snp" version="0.1">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">git clone --recursive https://github.com/ChrisD11/snp_caller.git</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>snp</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 snp finder requires a C++ compiler</readme>
+    </package>
+</tool_dependency>
diff -r 000000000000 -r 4b10ed36eb91 variant_caller.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_caller.xml	Mon Feb 22 19:43:25 2016 -0500
@@ -0,0 +1,60 @@
+<tool id="variant_caller" name="Snip Finder identifies snips from single-end and paired-end data" version="0.1.0">
+    <requirements>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+	$__tool_directory__/snp
+	    -amr_fp $input1
+	    #if $sam_type.mode == "single_end"
+	    -samse $sam_type.samse_input2
+	    $sam_type.best
+	    #else
+	    -sampe $sam_type.sampe_input2
+	    $sam_type.best
+	    #end if
+	    -out_fp $output1
+    ]]></command>
+    <inputs>
+	<param type="data" name="input1" format="fasta" label="Specify fasta file"/>
+	<conditional name="sam_type">
+	    <param name="mode" type="select" label="Specify sam file type">
+	        <option value="single_end"></option>
+		<option value="paired_end"></option>
+	    </param>
+	    <when value="single_end">
+	        <param type="data" name="samse_input2" format="sam" label="Single-end SAM file"/>
+		<param name="best" type="boolean" label="Filter on unique alignments"
+                       truevalue="-b" falsevalue="" />
+	    </when>
+	    <when value="paired_end">
+		<param type="data" name="sampe_input2" format="sam" label="Paired-end SAM file"/>
+		<param name="best" type="boolean" label="Filter on unique alignments"
+		       truevalue="-b" falsevalue="" />
+	    </when>
+	</conditional>
+    </inputs>
+    <outputs>
+	<data name="output1" format="tabular" />
+    </outputs>
+    <help><![CDATA[
+
+This program parses a SAM file and looks for single nucleotide polymorphisms (SNPs). In single-end mode, only alignments with bit four not set are considered. In paired-end mode, only reads that mapped in a proper pair are considered. When filtering on unique alignments, only alignments with the XT:A:U field are considered.
+
+Program: SNP Caller
+
+Contact: Chris Dean <cdean11@rams.colostate.edu>
+
+Usage: snp [options]
+
+Options:
+
+    -amr_fp	amr database path
+    -samse	single-end sam file path
+    -sampe	paired-end sam file path
+    -b		filter on unique alignments
+
+
+    ]]></help>
+</tool>