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Add ubu (UNC Bioinformatics Utilities)
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‎packages/package_ubu_1_2/tool_dependencies.xml

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<?xml version="1.0"?>
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<tool_dependency>
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<package name="ubu" version="1.2">
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<install version="1.0">
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<actions>
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<action type="download_by_url">https://github.com/mozack/ubu/releases/download/v1.2b/ubu-1.2b-SNAPSHOT-jar-with-dependencies.jar</action>
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<action type="move_directory_files">
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<source_directory>.</source_directory>
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<destination_directory>$INSTALL_DIR</destination_directory>
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</action>
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<action type="set_environment">
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<environment_variable name="UBU_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
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<environment_variable name="UBU_JAR" action="set_to">$INSTALL_DIR/ubu-1.2b-SNAPSHOT-jar-with-dependencies.jar</environment_variable>
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</action>
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</actions>
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</install>
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<readme></readme>
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</package>
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</tool_dependency>

‎ubu/test-data/sam2fastq_expected_paired1.fastq

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@XYZ13-SN749:180:D127FACXX:6:1101:1066:2717/1
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GTTNGTTTAAATCCTTGAGGGGTACAGCATCACTCGGATTCTGTGTCN
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@@B#4=DDHHHHGJHHIIJIJJBHG9EHGHIIJHGGIJIJIJJHHHF#
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@XYZ13-SN749:180:D127FACXX:6:1101:1066:12878/1
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GCTNGACCTTGATGGACAGACCAATAAGGGTGGCCATGCTGCAGTGCN
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@@=#4=BDHHHH:AFGFHCCGCHEGIIGIE:EFGH3:?DFIIIG9BF#
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@XYZ13-SN749:180:D127FACXX:6:1101:1066:130898/1
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CTTNTGCCTCAGCCTCCTGAGTGGCTGGGACTACAGGCACCCGCCACN
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+
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@@@#4=DDFHHFHIHHIIIII<FHGEGHG9B;DD<BDDDFHH>GHFE#
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@XYZ13-SN749:180:D127FACXX:6:1101:1067:49195/1
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GGCNTGTTTCGTTCCAACCTCTTGACCCAGGACAACGGCATTCTGACN
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+
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=<?#4=22CDD<ACE:CEFABFBFEFE@EEEIAD@?0:DDD9B8)8B#

‎ubu/test-data/sam2fastq_expected_paired2.fastq

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@XYZ13-SN749:180:D127FACXX:6:1101:1066:2717/2
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TTGGGCAAGAGATGCGCTTATGTATATAAAGCAAAGAACAACACAGTN
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BCCFFFFDHFGHHIJJJGHGHIFHHGEGIJIIJIIJJIJJIJJJJJG#
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@XYZ13-SN749:180:D127FACXX:6:1101:1066:12878/2
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CGCTAGAGGAGTTGAACGTAGTAGAGCAGGTGCGGGTTCAGGTTAGCN
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@@@DDDDFHFHABGHGHEACFA?BEGDGHI8EBFHI6BD?BB=BFFE#
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@XYZ13-SN749:180:D127FACXX:6:1101:1066:130898/2
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CTGCAATCCCAGCACTTTGGGGGGCCGAGGCGGGCGGGGCACCAGGTN
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@@BFFFFFHBFHHHIFBBIGHIGDBBBDDDDDB@##############
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@XYZ13-SN749:180:D127FACXX:6:1101:1067:49195/2
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CGCCCGCTCAATGTGGTCGTTGCCTTCGGCCTTGAGCTGAACGTGGTN
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;8;7;??A:)<DFC?C+2<CG;8?F@B))60BG0B9?GI<H@B=FG##

‎ubu/test-data/sam2fastq_test.sam

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@HD VN:1.0 SO:unsorted
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@SQ SN:chr1 LN:249250621
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@SQ SN:chr10 LN:135534747
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@SQ SN:chr11 LN:135006516
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@SQ SN:chr12 LN:133851895
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@SQ SN:chr13 LN:115169878
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@SQ SN:chr14 LN:107349540
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@SQ SN:chr15 LN:102531392
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@SQ SN:chr16 LN:90354753
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@SQ SN:chr17 LN:81195210
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@SQ SN:chr18 LN:78077248
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@SQ SN:chr19 LN:59128983
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@SQ SN:chr2 LN:243199373
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@SQ SN:chr20 LN:63025520
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@SQ SN:chr21 LN:48129895
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@SQ SN:chr22 LN:51304566
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@SQ SN:chr3 LN:198022430
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@SQ SN:chr4 LN:191154276
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@SQ SN:chr5 LN:180915260
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@SQ SN:chr6 LN:171115067
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@SQ SN:chr7 LN:159138663
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@SQ SN:chr8 LN:146364022
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@SQ SN:chr9 LN:141213431
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@SQ SN:chrM_rCRS LN:16569
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@SQ SN:chrX LN:155270560
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@SQ SN:chrY LN:59373566
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@RG ID:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG PL:illumina PU:barcode LB:TruSeq SM:120604_XYZ13-SN749_0180_BD127FACXX_6_GATCAG
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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:+
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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:+
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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
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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:-
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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
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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
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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
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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
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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
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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
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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
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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

‎ubu/tool_dependencies.xml

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<?xml version="1.0"?>
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<tool_dependency>
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<package name="ubu" version="1.2">
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<repository name="package_ubu_1_2" owner="jjohnson" />
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</package>
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</tool_dependency>

‎ubu/ubu_sam2fastq.xml

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<tool id="ubu_sam2fastq" name="UBU sam2fastq" version="0.1.0">
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<description>Convert a SAM/BAM file to FASTQ</description>
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<requirements>
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<requirement version="1.2">ubu</requirement>
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</requirements>
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<stdio>
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<exit_code range="1:" />
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</stdio>
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<command><![CDATA[
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java -Xmx1G -jar \$UBU_JAR sam2fastq --in $input --fastq1 paired1.fastq --fastq2 paired2.fastq --end1 '$end1' --end2 '$end2'
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]]></command>
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<inputs>
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<param name="input" type="data" format="sam,bam" label="Sam or Bam file to convert" />
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<param name="end1" type="text" value="/1" label="Id suffix used to identify the first read in a pair." />
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<param name="end2" type="text" value="/2" label="Id suffix used to identify the second read in a pair." />
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</inputs>
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<outputs>
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<data name="fastq1" format="data" from_work_dir="paired1.fastq" />
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<data name="fastq2" format="data" from_work_dir="paired2.fastq" />
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</outputs>
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<tests>
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<test>
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<param name="input" value="sam2fastq_test.sam" />
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<output name="fastq1" file="sam2fastq_expected_paired1.fastq"/>
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<output name="fastq2" file="sam2fastq_expected_paired2.fastq"/>
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</test>
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</tests>
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<help><![CDATA[
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input SAM/BAM file
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Option Description
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------ -----------
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--in Required input sam or bam file
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--fastq1 Required output FASTQ file
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--fastq2 Second FASTQ file for paired end
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--end1 Id suffix used to identify the first
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read in a pair. i.e. /1 (omit this
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option to use bit flag)
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--end2 Id suffix used to identify the second
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read in a pair. i.e. /2 (omit this
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option to use bit flag)
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]]></help>
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</tool>

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