# HG changeset patch
# User chrisd
# Date 1467268763 14400
# Node ID d612ce3827b9f44471d539f33d75107e5607fd9d
# Parent  d9be5a7e70f59b92bcb790bc113944c5ee951d91
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/snpfinder commit 60b005a83eab4984bc88a85a07ca2e416c3e507c-dirty

diff -r d9be5a7e70f5 -r d612ce3827b9 test-data/sampe_result
--- a/test-data/sampe_result	Wed Mar 23 18:04:21 2016 -0400
+++ b/test-data/sampe_result	Thu Jun 30 02:39:23 2016 -0400
@@ -1,4 +1,4 @@
-Chr,Haplotype,Frequency
+Gene,Haplotype Pattern,Occurrence
 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
diff -r d9be5a7e70f5 -r d612ce3827b9 test-data/samse_best_result
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samse_best_result	Thu Jun 30 02:39:23 2016 -0400
@@ -0,0 +1,1 @@
+Gene,Haplotype Pattern,Occurrence
diff -r d9be5a7e70f5 -r d612ce3827b9 test-data/samse_result
--- a/test-data/samse_result	Wed Mar 23 18:04:21 2016 -0400
+++ b/test-data/samse_result	Thu Jun 30 02:39:23 2016 -0400
@@ -1,4 +1,4 @@
-Chr,Haplotype,Frequency
+Gene,Haplotype Pattern,Occurrence
 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
diff -r d9be5a7e70f5 -r d612ce3827b9 variant_caller.xml
--- a/variant_caller.xml	Wed Mar 23 18:04:21 2016 -0400
+++ b/variant_caller.xml	Thu Jun 30 02:39:23 2016 -0400
@@ -8,49 +8,49 @@
     </stdio>
     <command><![CDATA[
 	snp
-	    -amr_fp $input1
+	    -amr_fp $reference
 	    #if $sam_type.mode == "single_end"
-	    -samse $sam_type.samse_input2
+	    -samse $sam_type.samse_input
 	    $sam_type.best
 	    #else
-	    -sampe $sam_type.sampe_input2
+	    -sampe $sam_type.sampe_input
 	    $sam_type.best
 	    #end if
-	    -out_fp $output1
+	    -out_fp $result
     ]]></command>
     <inputs>
-	<param type="data" name="input1" format="fasta" label="Reference sequence"/>
+	<param type="data" name="reference" 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="" />
+	        <param type="data" name="samse_input" 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="" />
+		<param type="data" name="sampe_input" 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" />
+	<data name="result" 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>
+	    <param name="mode" value="single_end"/>
+            <param name="reference" value="ref.fa"/>
+            <param name="samse_input" value="samse.sam"/>
+            <output name="result" file="samse_result" ftype="tabular"/>
         </test>
-        <test>
-            <param name="input1" value="ref.fa"/>
-	    <param name="sam_type.sampe_input2" value="sampe.sam"/>
-	    <output name="output1" value="sampe_result"/>
-        </test>
+	<test>
+	    <param name="mode" value="paired_end"/>
+	    <param name="reference" value="ref.fa"/>
+	    <param name="sampe_input" value="sampe.sam"/>
+	    <output name="result" file="sampe_result" ftype="tabular"/>
+	</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.