# HG changeset patch
# User devteam
# Date 1447264312 18000
# Node ID 881e16ad05c65f49a9878d020299fb76f8748708
# Parent  d04d9f1c679140c23f333bb2ea63985a54fd5385
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/sam_to_bam commit a1517c9d22029095120643bbe2c8fa53754dd2b7

diff -r d04d9f1c6791 -r 881e16ad05c6 sam_to_bam.xml
--- a/sam_to_bam.xml	Tue Apr 21 14:52:20 2015 -0400
+++ b/sam_to_bam.xml	Wed Nov 11 12:51:52 2015 -0500
@@ -1,22 +1,21 @@
-<tool id="sam_to_bam" name="SAM-to-BAM" version="2.0">
+<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1">
   <description>convert SAM to BAM</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"></expand>
+  <expand macro="stdio"></expand>
   <expand macro="version_command"></expand>
-  <expand macro="stdio"></expand>
   <command>
     <![CDATA[
-        samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o sorted_input.bam -T temp "$input1" && 
-          #if $source.index_source == "history":
-            ln -s $source.ref_file input.fa &&
-            samtools faidx input.fa &&
-          #else
-            ln -s ${source.index.fields.path} input.fa &&
-            ln -s ${source.index.fields.path}.fai input.fa.fai &&
-          #end if
-          samtools view -@ \${GALAXY_SLOTS:-1} -b -h -o $output1 -T input.fa sorted_input.bam
+        #if $source.index_source == "history":
+          ln -s $source.ref_file input.fa &&
+          samtools faidx input.fa &&
+        #else
+          ln -s ${source.index.fields.path} input.fa &&
+          ln -s ${source.index.fields.path}.fai input.fa.fai &&
+        #end if
+        samtools view -b -@ \${GALAXY_SLOTS:-1} -t input.fa.fai "$input1" | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o "$output1" -T temp
     ]]>
     </command>
     <inputs>
@@ -68,6 +67,12 @@
             <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
             <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" />
         </test>
+        <test>
+            <param name="index_source" value="history" />
+            <param name="input1" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
+            <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
+            <output file="sam_to_bam_out3.bam" ftype="bam" name="output1" />
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r d04d9f1c6791 -r 881e16ad05c6 test-data/sam_to_bam_noheader_in2.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam_to_bam_noheader_in2.sam	Wed Nov 11 12:51:52 2015 -0500
@@ -0,0 +1,10 @@
+HWI-EAS91_1_30788AAXX:1:1:1513:715	16	chrM	9563	25	36M	*	0	0	CTGACTACCACAACTAAACATCTATGCNNAAAAAAC	I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1698:516	16	chrM	2735	25	36M	*	0	0	TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC	I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1491:637	16	chrM	10864	25	36M	*	0	0	TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC	DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1711:249	16	chrM	10617	25	36M	*	0	0	ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1634:211	0	chrM	9350	25	36M	*	0	0	GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1218:141	16	chrM	14062	25	36M	*	0	0	ACAAAACTAACAACAAAAATAACACTCNNAATAAAC	I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1398:854	16	chrM	3921	25	36M	*	0	0	CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC	IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1310:991	16	chrM	10002	25	36M	*	0	0	CTCCTATGCCTAGAAGGAATAATACTANNACTATTC	I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1716:413	0	chrM	6040	25	36M	*	0	0	GATCCAANNCTTTATCAACACCTATTCTGATTCTTC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
+HWI-EAS91_1_30788AAXX:1:1:1630:59	16	chrM	12387	25	36M	*	0	0	TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC	FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII	NM:i:1	X1:i:1	MD:Z:7N0N27	RG:Z:rg1
diff -r d04d9f1c6791 -r 881e16ad05c6 test-data/sam_to_bam_out3.bam
Binary file test-data/sam_to_bam_out3.bam has changed
diff -r d04d9f1c6791 -r 881e16ad05c6 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 21 14:52:20 2015 -0400
+++ b/tool_dependencies.xml	Wed Nov 11 12:51:52 2015 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="1.2">
-        <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>