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changeset 0:d9be5a7e70f5 draft

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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/snpfinder commit 8b7c17352f46ab4fce3bc13c3e63d4021fe83ae7
author chrisd
date Wed, 23 Mar 2016 18:04:21 -0400
parents
children d612ce3827b9
files test-data/ref.fa test-data/sampe.sam test-data/sampe_result test-data/samse.sam test-data/samse_result tool_dependencies.xml variant_caller.xml
diffstat 7 files changed, 144 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref.fa	Wed Mar 23 18:04:21 2016 -0400
@@ -0,0 +1,2 @@
+>chr2:172936693-172938111
+TTATGGCTTTAAAAATATTGTAACAGTGTCTGAATCAAACTTTAGTAAAATCTCTTTGGGTTATATCTGAGAAGCTTTTATTGAAGACTTTGAACAAAATTGTGTTTTTGACAGTTTTAAATTATAGGCTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACTATCTTACTGTCCATGAATATAATAGAAATGAATTCAAAATGCAGTTTTATTTTTGCAAATGGGATGAGTCGATAGATGCACCTCATATTTTTGAACACCTAGGGTTCAACAAATTTACTGGTGGTGCTCTTGCATTTTAACAAAATTTATTCTTCAGTAGAAGGGGGCAGAGAACACTAGATTCTTATTCAAGCATTCTATCGAGCTCTGCATTCATGGCTGTGTCTAAAGGGCATGTCAGCCTTTGATTCTCTCTGAGAGGTAATTATCCTTTTCCTGTCACGGAACAACAAATGATAGCTAACTACAGAGGCACATTTGCAGTAGTCACATTCATCAACTGCAGAAAAAAAAATTCAATTTAATTGTGCAACACAGCTGCACATGGGCTTTTGAGCATTTCTGTTGTTCTCCCTGTCTCGCTATTCCTCCCTCCAGATCTATTTTTTAAACTTTTTTTCTGGTTATTTTTTCCCCTTTTTGTCTCTTCTTCCATTTTTACTCTCTGTACTTTCTTGTTAAAGTAATTTTCCTTTGTGGCTCTCATTCTTTTTCCCCCATTGAAGGCTATGAATGTAGAAAATTATCACAATTACTCATATAATTGAGCCTCTTTGTAGCAAGTGCAACTCCAGTAGCCTTTCTCCATCATGAAAATGGTTTCATTATAGGGTTTTTCATATTCTCTGACACCATCTACACAGAGGAACAGGCGTGCAGATGAGATGTGCTAGGAACAGGCTAGATCAGTAAGGTCACAGTAGGAATAATTAGCTCTGCTATGGAAAGAGCATCTAGGCCTTTTACTGCTACATAAATGTACTGTCCATGGCTTTTAGTCACAAAAAAAACTTACTAACAAATGGAGCTCCCGCCTACTACTTTGAAAAAAAGATTTGTATCAACACTACAATTTTCCATCATTAAGACTAATAACACAGAGCCTAGTATACATCAAGGGGAATAAAAAGAAAAATCTCACATTCAAGTGGCGGCTGGGTGCTGACCTTTGTTCCCTTTTTTTGTGTACGACTTAACTCTTTACAAAAAAGAGCCACACGCCACACCAACATGCAGGTGAACTCCAGCTAGTACTAGCAAAGCATAGCATTCAGTTGGAAAATTTGATAAATCTCCATGCAGGATAATGCATTTCATTACATATTCACTACATTAATTCTAGCTACATT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampe.sam	Wed Mar 23 18:04:21 2016 -0400
@@ -0,0 +1,22 @@
+@SQ	SN:chr2:172936693-172938111	LN:1418
+@PG	ID:bwa	PN:bwa	VN:0.7.12-r1039	CL:bwa sampe ref.fa forward.sai reverse.sai lane1.fq lane2.fq
+chr2:172936693-172938111_82_621_1:0:0_0:0:0_0	81	chr2:172936693-172938111	552	37	70M	=	82	-540	GTAGTCACATTCATCAACTGCAGAAAAAAAAATTCAATTTAATTGTGCAACACAGCTGCACATGGGCTTT	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:70
+chr2:172936693-172938111_82_621_1:0:0_0:0:0_0	161	chr2:172936693-172938111	82	37	70M	=	552	540	TGAAGACTTTGAACCAAATTGTGTTTTTGACAGTTTTAAATTATAGGCTAACTAGCCTGGGAAAAAAGGA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:14A55
+chr2:172936693-172938111_127_617_0:0:0_2:0:0_1	99	chr2:172936693-172938111	127	60	70M	=	548	491	GGCTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCT	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:70
+chr2:172936693-172938111_127_617_0:0:0_2:0:0_1	147	chr2:172936693-172938111	548	60	70M	=	127	-491	TGCAGTAGTCACATTCATCAACTGCAGAAAAAAAAATTCAAGTTAATGGTGCAACACAGCTGCACATGGG	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:2	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:41T5T22
+chr2:172936693-172938111_695_1174_2:0:0_0:0:0_2	83	chr2:172936693-172938111	1105	60	70M	=	695	-480	TACTACTTTGAAAAAAAGATTTGTATCAACACTACAATTTTCCATCATTAAGACTAATAACACAGAGCCT	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:70
+chr2:172936693-172938111_695_1174_2:0:0_0:0:0_2	163	chr2:172936693-172938111	695	60	70M	=	1105	480	ATTTTTTCCCCTTTTTGTCTGTTCTTCCATTTTTACTCTCTGTACTTTCTTGTAAAAGTAATTTTCCTTT	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:2	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:20C32T16
+chr2:172936693-172938111_675_1201_1:0:0_1:0:0_3	97	chr2:172936693-172938111	675	37	70M	=	1132	527	TTTAAACTTTTTTTCTGGTTATTTTTTCCCCTTTTTGTCTCTTCTTCCATTTTTACTCTCTGTACTTTGT	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:68C1
+chr2:172936693-172938111_675_1201_1:0:0_1:0:0_3	145	chr2:172936693-172938111	1132	37	70M	=	675	-527	AACACTACAATTTTCCATCTTTAAGACTAATAACACAGAGCCTAGTATACATCAAGGGGAATAAAAAGAA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:19A50
+chr2:172936693-172938111_133_602_2:0:0_0:0:0_4	99	chr2:172936693-172938111	133	60	70M	=	533	470	CTCGCGTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGG	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:2	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:2A2C64
+chr2:172936693-172938111_133_602_2:0:0_0:0:0_4	147	chr2:172936693-172938111	533	60	70M	=	133	-470	CTACAGAGGCACATTTGCAGTAGTCACATTCATCAACTGCAGAAAAAAAAATTCAATTTAATTGTGCAAC	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:70
+chr2:172936693-172938111_268_735_1:0:0_1:0:0_5	83	chr2:172936693-172938111	666	60	70M	=	268	-468	CATCTATTTTTTAAACTTTTTTTCTGGTTATTTTTTCCCCTTTTTGTCTCTTCTTCCATTTTTACTCTCT	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:0G69
+chr2:172936693-172938111_268_735_1:0:0_1:0:0_5	163	chr2:172936693-172938111	268	60	70M	=	666	468	TGCAGATTTATTTTTGCAAATGGGATGAGTCGATAGATGCACCTCATATTTTTGAACACCTAGGGTTCAA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:5T64
+chr2:172936693-172938111_380_811_2:0:0_1:0:0_6	99	chr2:172936693-172938111	380	60	70M	=	742	432	CTTCAGTAGAAGGGGGCAGAGAACACTAGCTTCTTCTTCAAGCATTCTATCGAGCTCTGCATTCATGGCT	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:2	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:29A5A34
+chr2:172936693-172938111_380_811_2:0:0_1:0:0_6	147	chr2:172936693-172938111	742	60	70M	=	380	-432	TCTTGTTAAAGTAATTTTCCTTTGTGGCTCTCATTCTTTTTCCCCCATTGAAGGCTAGGAATGTAGAAAA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:57T12
+chr2:172936693-172938111_440_981_0:0:0_0:0:0_7	81	chr2:172936693-172938111	912	37	70M	=	440	-542	TCTCTGACACCATCTACACAGAGGAACAGGCGTGCAGATGAGATGTGCTAGGAACAGGCTAGATCAGTAA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:70
+chr2:172936693-172938111_440_981_0:0:0_0:0:0_7	161	chr2:172936693-172938111	440	37	70M	=	912	542	ATTCATGGCTGTGTCTAAAGGGCATGTCAGCCTTTGATTCTCTCTGAGAGGTAATTATCCTTTTCCTGTC	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:70
+chr2:172936693-172938111_59_532_2:0:0_2:0:0_8	83	chr2:172936693-172938111	463	60	70M	=	59	-474	ATGGCAGCCTTTGATTCTCTCTGAGAGGTAATTTTCCTTTTCCTGTCACGGAACAACAAATGATAGCTAA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:2	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:3T29A36
+chr2:172936693-172938111_59_532_2:0:0_2:0:0_8	163	chr2:172936693-172938111	59	60	70M	=	463	474	GGTTATATCTGAGAAGCTTTTATTGAAGACTTTGAACAAAATTGTGTTTTTGACAGTTTTCAATTATCGG	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:2	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:60A6A2
+chr2:172936693-172938111_642_1121_0:0:0_3:0:0_9	83	chr2:172936693-172938111	1052	60	70M	=	642	-480	GGTCCATGGCTTTTAGTCACAAAAAAAACTTAATAACAAATGGAGCTCCCCCCTACTACTTTGAAAAAAA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:3	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:3	XO:i:0	XG:i:0	MD:Z:0T31C17G19
+chr2:172936693-172938111_642_1121_0:0:0_3:0:0_9	163	chr2:172936693-172938111	642	60	70M	=	1052	480	CCTGTCTCGCTATTCCTCCCTCCAGATCTATTTTTTAAACTTTTTTTCTGGTTATTTTTTCCCCTTTTTG	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:70
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampe_result	Wed Mar 23 18:04:21 2016 -0400
@@ -0,0 +1,8 @@
+Chr,Haplotype,Frequency
+chr2:172936693-172938111,1052T->G:1084C->A:1102G->C:,1
+chr2:172936693-172938111,119A->C:126A->C:466T->G:496A->T:,1
+chr2:172936693-172938111,135A->C:138C->G:,1
+chr2:172936693-172938111,273T->A:666G->C:,1
+chr2:172936693-172938111,409A->C:415A->C:799T->G:,1
+chr2:172936693-172938111,589T->G:595T->G:,1
+chr2:172936693-172938111,715C->G:748T->A:,1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samse.sam	Wed Mar 23 18:04:21 2016 -0400
@@ -0,0 +1,12 @@
+@SQ	SN:chr2:172936693-172938111	LN:1418
+@PG	ID:bwa	PN:bwa	VN:0.7.12-r1039	CL:bwa samse ref.fa aln_sa.sai lane1.fq
+chr2:172936693-172938111_860_1331_0:0:0_1:0:0_0	0	chr2:172936693-172938111	860	37	70M	*	0	0	CCAGTAGCCTTTCTCCATCATGAAAATGGTTTCATTATAGGGTTTTTCATATTCTCTGACACCATCTACA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:70
+chr2:172936693-172938111_732_1257_1:0:0_4:0:0_1	0	chr2:172936693-172938111	732	37	70M	*	0	0	CTCTGAACTTTCTTGTTAAAGTAATTTTCCTTTGTGGCTCTCATTCTTTTTCCCCCATTGAAGGCTATGA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:5T64
+chr2:172936693-172938111_742_1203_2:0:0_2:0:0_2	16	chr2:172936693-172938111	1134	37	70M	*	0	0	CACTACAATTTTCCATCATTAAGACTAATAACACAGAGCCTAGTATAAATCAAGGGCAATAAAAAGAAAA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:47C8G13
+chr2:172936693-172938111_198_767_3:0:0_2:0:0_3	0	chr2:172936693-172938111	198	37	70M	*	0	0	CTGGGAAAAGAAATTAAATGCATATCTCACTATCTTACTGTCCAAGAATATAATAGAAAAGAATTCAAAA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:0	XG:i:0	MD:Z:15T28T14T10
+chr2:172936693-172938111_453_1032_2:0:0_1:0:0_4	0	chr2:172936693-172938111	453	37	70M	*	0	0	TCTAAAGGGCATGTCATCCTTAGATTCTCTCTGAGAGGTAATTATCCTTTTCCTGTCACGGAACAACAAA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:16G4T48
+chr2:172936693-172938111_49_530_3:0:0_2:0:0_5	0	chr2:172936693-172938111	49	37	70M	*	0	0	AAACTCTTTGGGTTATATCTGAGAATCTTTTATTGAAGACTTTGAACAAAATTGTGTTTTTGACATTTTT	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:0	XG:i:0	MD:Z:2T22G39G4
+chr2:172936693-172938111_148_725_2:0:0_1:0:0_6	16	chr2:172936693-172938111	656	37	70M	*	0	0	CCTCCCTCCAGATCTTTTTTTTAAACTTTTTTTCTGGTTATTTTTTCCCCTTTTTGTCTCTTCTTCCATT	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:15A54
+chr2:172936693-172938111_198_788_0:0:0_0:0:0_7	0	chr2:172936693-172938111	198	37	70M	*	0	0	CTGGGAAAAGAAATTTAATGCATATCTCACTATCTTACTGTCCATGAATATAATAGAAATGAATTCAAAA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:70
+chr2:172936693-172938111_839_1328_2:0:0_3:0:0_8	16	chr2:172936693-172938111	1259	37	70M	*	0	0	GACTGAACTCTTTACAAAAAAGAGCCACACGCCACACCAACATGCTGGTGTACTCCAGCTAGTACTAGCA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:0	XG:i:0	MD:Z:4T40A4A19
+chr2:172936693-172938111_892_1355_1:0:0_0:0:0_9	0	chr2:172936693-172938111	892	37	70M	*	0	0	CATTATAGGGTTTTTCATATTCTCTGACACCATCTACACAGAGGAACAGGCGTGCAGCTGAGATGTGCTA	2222222222222222222222222222222222222222222222222222222222222222222222	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:57A12
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samse_result	Wed Mar 23 18:04:21 2016 -0400
@@ -0,0 +1,9 @@
+Chr,Haplotype,Frequency
+chr2:172936693-172938111,1181C->A:1190G->C:,1
+chr2:172936693-172938111,1263T->G:1304A->T:1309A->T:,1
+chr2:172936693-172938111,213T->A:242T->A:257T->A:,1
+chr2:172936693-172938111,469G->T:474T->A:,1
+chr2:172936693-172938111,51T->A:74G->T:114G->T:,1
+chr2:172936693-172938111,671A->T:,1
+chr2:172936693-172938111,737T->A:,1
+chr2:172936693-172938111,949A->C:,1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Mar 23 18:04:21 2016 -0400
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="snp_caller" 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_caller.xml	Wed Mar 23 18:04:21 2016 -0400
@@ -0,0 +1,72 @@
+<tool id="snp_caller" name="Snip Finder" version="0.1.0">
+    <description>Identifies snips for both single-end and paired-end data</description>
+    <requirements>
+        <requirement type="package" version="0.1">snp_caller</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+	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="Reference sequence"/>
+	<conditional name="sam_type">
+	    <param name="mode" type="select" label="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>
+    <tests>
+        <test>
+            <param name="input1" value="ref.fa"/>
+            <param name="sam_type.samse_input2" value="samse.sam"/>
+	    <output name="output1" value="samse_result"/>
+        </test>
+        <test>
+            <param name="input1" value="ref.fa"/>
+	    <param name="sam_type.sampe_input2" value="sampe.sam"/>
+	    <output name="output1" value="sampe_result"/>
+        </test>
+    </tests>
+    <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: snpfinder
+
+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>
+    <citations>
+    </citations>
+</tool>