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changeset 0:aa2cf6718319 draft default tip

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author jjohnson
date Mon, 02 Nov 2015 08:48:24 -0500
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files test-data/sam2fastq_expected_paired1.fastq test-data/sam2fastq_expected_paired2.fastq test-data/sam2fastq_test.sam tool_dependencies.xml ubu_sam2fastq.xml
diffstat 5 files changed, 122 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam2fastq_expected_paired1.fastq	Mon Nov 02 08:48:24 2015 -0500
@@ -0,0 +1,16 @@
+@XYZ13-SN749:180:D127FACXX:6:1101:1066:2717/1
+GTTNGTTTAAATCCTTGAGGGGTACAGCATCACTCGGATTCTGTGTCN
++
+@@B#4=DDHHHHGJHHIIJIJJBHG9EHGHIIJHGGIJIJIJJHHHF#
+@XYZ13-SN749:180:D127FACXX:6:1101:1066:12878/1
+GCTNGACCTTGATGGACAGACCAATAAGGGTGGCCATGCTGCAGTGCN
++
+@@=#4=BDHHHH:AFGFHCCGCHEGIIGIE:EFGH3:?DFIIIG9BF#
+@XYZ13-SN749:180:D127FACXX:6:1101:1066:130898/1
+CTTNTGCCTCAGCCTCCTGAGTGGCTGGGACTACAGGCACCCGCCACN
++
+@@@#4=DDFHHFHIHHIIIII<FHGEGHG9B;DD<BDDDFHH>GHFE#
+@XYZ13-SN749:180:D127FACXX:6:1101:1067:49195/1
+GGCNTGTTTCGTTCCAACCTCTTGACCCAGGACAACGGCATTCTGACN
++
+=<?#4=22CDD<ACE:CEFABFBFEFE@EEEIAD@?0:DDD9B8)8B#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam2fastq_expected_paired2.fastq	Mon Nov 02 08:48:24 2015 -0500
@@ -0,0 +1,16 @@
+@XYZ13-SN749:180:D127FACXX:6:1101:1066:2717/2
+TTGGGCAAGAGATGCGCTTATGTATATAAAGCAAAGAACAACACAGTN
++
+BCCFFFFDHFGHHIJJJGHGHIFHHGEGIJIIJIIJJIJJIJJJJJG#
+@XYZ13-SN749:180:D127FACXX:6:1101:1066:12878/2
+CGCTAGAGGAGTTGAACGTAGTAGAGCAGGTGCGGGTTCAGGTTAGCN
++
+@@@DDDDFHFHABGHGHEACFA?BEGDGHI8EBFHI6BD?BB=BFFE#
+@XYZ13-SN749:180:D127FACXX:6:1101:1066:130898/2
+CTGCAATCCCAGCACTTTGGGGGGCCGAGGCGGGCGGGGCACCAGGTN
++
+@@BFFFFFHBFHHHIFBBIGHIGDBBBDDDDDB@##############
+@XYZ13-SN749:180:D127FACXX:6:1101:1067:49195/2
+CGCCCGCTCAATGTGGTCGTTGCCTTCGGCCTTGAGCTGAACGTGGTN
++
+;8;7;??A:)<DFC?C+2<CG;8?F@B))60BG0B9?GI<H@B=FG##
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam2fastq_test.sam	Mon Nov 02 08:48:24 2015 -0500
@@ -0,0 +1,39 @@
+@HD	VN:1.0	SO:unsorted
+@SQ	SN:chr1	LN:249250621
+@SQ	SN:chr10	LN:135534747
+@SQ	SN:chr11	LN:135006516
+@SQ	SN:chr12	LN:133851895
+@SQ	SN:chr13	LN:115169878
+@SQ	SN:chr14	LN:107349540
+@SQ	SN:chr15	LN:102531392
+@SQ	SN:chr16	LN:90354753
+@SQ	SN:chr17	LN:81195210
+@SQ	SN:chr18	LN:78077248
+@SQ	SN:chr19	LN:59128983
+@SQ	SN:chr2	LN:243199373
+@SQ	SN:chr20	LN:63025520
+@SQ	SN:chr21	LN:48129895
+@SQ	SN:chr22	LN:51304566
+@SQ	SN:chr3	LN:198022430
+@SQ	SN:chr4	LN:191154276
+@SQ	SN:chr5	LN:180915260
+@SQ	SN:chr6	LN:171115067
+@SQ	SN:chr7	LN:159138663
+@SQ	SN:chr8	LN:146364022
+@SQ	SN:chr9	LN:141213431
+@SQ	SN:chrM_rCRS	LN:16569
+@SQ	SN:chrX	LN:155270560
+@SQ	SN:chrY	LN:59373566
+@RG	ID:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG	PL:illumina	PU:barcode	LB:TruSeq	SM:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG
+XYZ13-SN749:180:D127FACXX:6:1101:1066:2717/1	83	chr3	197681001	63	18M1602N30M	=	197678145	-4506	NGACACAGAATCCGAGTGATGCTGTACCCCTCAAGGATTTAAACNAAC	#FHHHJJIJIJIGGHJIIHGHE9GHBJJIJIIHHJGHHHHDD=4#B@@	XF:Z:GTAG,	RG:Z:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG	IH:i:1	HI:i:1	NM:i:2	XS:A:+
+XYZ13-SN749:180:D127FACXX:6:1101:1066:2717/2	163	chr3	197678145	64	38M2691N10M	=	197681001	4506	TTGGGCAAGAGATGCGCTTATGTATATAAAGCAAAGAACAACACAGTN	BCCFFFFDHFGHHIJJJGHGHIFHHGEGIJIIJIIJJIJJIJJJJJG#	XF:Z:GTAG,	RG:Z:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG	IH:i:1	HI:i:1	NM:i:1	XS:A:+
+XYZ13-SN749:180:D127FACXX:6:1101:1066:12878/1	99	chr16	66967546	63	48M	=	66967636	385	GCTNGACCTTGATGGACAGACCAATAAGGGTGGCCATGCTGCAGTGCN	@@=#4=BDHHHH:AFGFHCCGCHEGIIGIE:EFGH3:?DFIIIG9BF#	RG:Z:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG	IH:i:1	HI:i:1	NM:i:2
+XYZ13-SN749:180:D127FACXX:6:1101:1066:12878/2	147	chr16	66967636	64	7M247N41M	=	66967546	-385	NGCTAACCTGAACCCGCACCTGCTCTACTACGTTCAACTCCTCTAGCG	#EFFB=BB?DB6IHFBE8IHGDGEB?AFCAEHGHGBAHFHFDDDD@@@	XF:Z:CTAC,	RG:Z:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG	IH:i:1	HI:i:1	NM:i:1	XS:A:-
+XYZ13-SN749:180:D127FACXX:6:1101:1066:130898/1	4	*	0	0	*	*	0	0	CTTNTGCCTCAGCCTCCTGAGTGGCTGGGACTACAGGCACCCGCCACN	@@@#4=DDFHHFHIHHIIIII<FHGEGHG9B;DD<BDDDFHH>GHFE#	RG:Z:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG
+XYZ13-SN749:180:D127FACXX:6:1101:1066:130898/2	4	*	0	0	*	*	0	0	CTGCAATCCCAGCACTTTGGGGGGCCGAGGCGGGCGGGGCACCAGGTN	@@BFFFFFHBFHHHIFBBIGHIGDBBBDDDDDB@##############	RG:Z:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG
+XYZ13-SN749:180:D127FACXX:6:1101:1067:49195/1	355	chr16	14972632	63	48M	=	14976463	3879	GGCNTGTTTCGTTCCAACCTCTTGACCCAGGACAACGGCATTCTGACN	=<?#4=22CDD<ACE:CEFABFBFEFE@EEEIAD@?0:DDD9B8)8B#	RG:Z:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG	IH:i:3	HI:i:3	NM:i:2
+XYZ13-SN749:180:D127FACXX:6:1101:1067:49195/1	99	chr16	16371281	63	48M	=	16375108	3875	GGCNTGTTTCGTTCCAACCTCTTGACCCAGGACAACGGCATTCTGACN	=<?#4=22CDD<ACE:CEFABFBFEFE@EEEIAD@?0:DDD9B8)8B#	RG:Z:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG	IH:i:3	HI:i:1	NM:i:2
+XYZ13-SN749:180:D127FACXX:6:1101:1067:49195/1	339	chr16	18528523	63	48M	=	18524696	-3875	NGTCAGAATGCCGTTGTCCTGGGTCAAGAGGTTGGAACGAAACANGCC	#B8)8B9DDD:0?@DAIEEE@EFEFBFBAFEC:ECA<DDC22=4#?<=	RG:Z:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG	IH:i:3	HI:i:2	NM:i:2
+XYZ13-SN749:180:D127FACXX:6:1101:1067:49195/2	401	chr16	14976463	60	48M	=	14972632	-3879	NACCACGTTCAGCTCAAGGCCGAAGGCAACGACCACATTGAGCGGGCG	##GF=B@H<IG?9B0GB06))B@F?8;GC<2+C?CFD<):A??;7;8;	RG:Z:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG	IH:i:3	HI:i:3	NM:i:2
+XYZ13-SN749:180:D127FACXX:6:1101:1067:49195/2	147	chr16	16375108	60	48M	=	16371281	-3875	NACCACGTTCAGCTCAAGGCCGAAGGCAACGACCACATTGAGCGGGCG	##GF=B@H<IG?9B0GB06))B@F?8;GC<2+C?CFD<):A??;7;8;	RG:Z:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG	IH:i:3	HI:i:1	NM:i:2
+XYZ13-SN749:180:D127FACXX:6:1101:1067:49195/2	417	chr16	18524696	60	48M	=	18528523	3875	CGCCCGCTCAATGTGGTCGTTGCCTTCGGCCTTGAGCTGAACGTGGTN	;8;7;??A:)<DFC?C+2<CG;8?F@B))60BG0B9?GI<H@B=FG##	RG:Z:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG	IH:i:3	HI:i:2	NM:i:2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Nov 02 08:48:24 2015 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ubu" version="1.2">
+        <repository changeset_revision="7ffcbcfeb42f" name="package_ubu_1_2" owner="jjohnson" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ubu_sam2fastq.xml	Mon Nov 02 08:48:24 2015 -0500
@@ -0,0 +1,45 @@
+<tool id="ubu_sam2fastq" name="UBU sam2fastq" version="0.1.0">
+    <description>Convert a SAM/BAM file to FASTQ</description>
+
+    <requirements>
+        <requirement version="1.2">ubu</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+    <command><![CDATA[
+        java -Xmx1G -jar \$UBU_JAR sam2fastq --in $input --fastq1 paired1.fastq --fastq2 paired2.fastq --end1 '$end1' --end2 '$end2'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="sam,bam" label="Sam or Bam file to convert" />
+        <param name="end1" type="text" value="/1" label="Id suffix used to identify the first read in a pair." />
+        <param name="end2" type="text" value="/2" label="Id suffix used to identify the second read in a pair." />
+    </inputs>
+    <outputs>
+        <data name="fastq1" format="data" from_work_dir="paired1.fastq" />
+        <data name="fastq2" format="data" from_work_dir="paired2.fastq" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="sam2fastq_test.sam" />
+            <output name="fastq1" file="sam2fastq_expected_paired1.fastq"/>
+            <output name="fastq2" file="sam2fastq_expected_paired2.fastq"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        input SAM/BAM file
+Option                                  Description                            
+------                                  -----------                            
+--in                                    Required input sam or bam file         
+--fastq1                                Required output FASTQ file             
+--fastq2                                Second FASTQ file for paired end       
+--end1                                  Id suffix used to identify the first   
+                                          read in a pair.  i.e. /1 (omit this  
+                                          option to use bit flag)              
+--end2                                  Id suffix used to identify the second  
+                                          read in a pair.  i.e. /2 (omit this  
+                                          option to use bit flag)              
+
+    ]]></help>
+</tool>