| Previous changeset 7:c7620aa7e1f0 (2017-05-10) Next changeset 9:6c60903f70ac (2017-07-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 39ca11da7daeb3fa030fcb28e8987f8d7f24aec3 |
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modified:
fastq_dump.xml test-data/DRR015708_forward.fastqsanger test-data/DRR015708_reverse.fastqsanger test-data/ERR027433_forward.fastqsanger test-data/ERR027433_reverse.fastqsanger test-data/SRR1993644.fastqsanger test-data/fastq_dump_result.fastq test-data/fastq_dump_result.fastq.gz |
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| diff -r c7620aa7e1f0 -r 1920e0508831 fastq_dump.xml --- a/fastq_dump.xml Wed May 10 10:45:41 2017 -0400 +++ b/fastq_dump.xml Mon Jul 03 06:30:15 2017 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="fastq_dump" name="Extract reads in Fastq/a" version="@VERSION@.2"> +<tool id="fastq_dump" name="Extract reads in Fastq/a" version="@VERSION@.3"> <description>format from NCBI SRA</description> <macros> <import>sra_macros.xml</import> @@ -49,6 +49,7 @@ --split-files #end if --defline-seq '@\$sn[_\$rn]/\$ri' + --defline-qual '+' $adv.split #if str( $adv.alignments ) == "aligned": |
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| diff -r c7620aa7e1f0 -r 1920e0508831 test-data/DRR015708_forward.fastqsanger --- a/test-data/DRR015708_forward.fastqsanger Wed May 10 10:45:41 2017 -0400 +++ b/test-data/DRR015708_forward.fastqsanger Mon Jul 03 06:30:15 2017 -0400 |
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| @@ -1,20 +1,20 @@ @HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/1 NTATTGTAGCGCACTATGAGGTCGCTCATTANTNTACATCNNCATCCAAATTTCAGCATNANTTTNNNNNTGTTTGATATTCTCAAAGNGATNAACGTTT -+DRR015708.1 HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938 length=100 ++ #1=DDFFFHGHHHJIIIIGIJFHIJJJJJJI#0#08DFII##-7@FHIIJJJJGEHEEE#,#,,;#####,,;?DCCDEFEEFCDDDD#+2+#+2<?<CC @HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/1 NTTCTAAACTCATTCCAGAAGTAATTGATGCGTCACCAATAATTGCAATATGTTTTCTATTGATTTGATTGATTTTATCTGCTGTTGCCATCCCAACAAT -+DRR015708.2 HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930 length=100 ++ #4=DDFFFHHHHHJJJJJJIIHIJJJJJJJJIHJJJJJIJJJJJJJJJJJJJIJJJJJJJJJJJJJJIIIICHHGEHHGIFEHHHHFFDFFFDDCEB@AC @HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/1 NTCACCTACAACTCGAATATTCGAATGATATGTGATATTGTTAGATGATTTTGGCATGCTTGCAGAAAGTGCATAAACACCTGTATTGATTCCCGAATTT -+DRR015708.3 HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936 length=100 ++ #4=DFFFFHHHHHIJIJJIHIIJIIJJJJIJIHIIGGIIJHIEHGGHGHIIJJJIIJJJJJHHCHGGGE@FHGHIIJIEHHEDCCDCCDEEED@AB/=A# @HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/1 NCTTAAAACTTATTAAATGAATCAATTAGATAAAAGACTTTTTTTGTTAGATGCTTATGCCTTAATTTTTAGAGGATATTATGCATTTATCAAAAATCCA -+DRR015708.4 HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864 length=100 ++ #4=DFFFFHHHHHJJJIJJJJJJJJJJJJJJJJIHGDGHIJJJJJJGHHJGIJIJJJJJJJIJIJJJJJHFFHGFDDFEEFEECCEEDEEDDCC3<A5>C @HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/1 NTAAAGGTTATTGTGCTTCACAGAAAATGCATTATTATGGGTATAAACTTCATGCGGTTTGCTCAGCGGAAGGTGTCTTTCAAAGTTTGGATATTAGTCC -+DRR015708.5 HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887 length=100 ++ #1=DDFFEHHHHHGIJJJJGIJJJJJJJJJJJJIJJJJJJJCFGFIIHJIJHIJJJJHIJJJJIJIJIFHBDE;@ACEEEDDCCCCCDDDCCDCCFECCC |
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| diff -r c7620aa7e1f0 -r 1920e0508831 test-data/DRR015708_reverse.fastqsanger --- a/test-data/DRR015708_reverse.fastqsanger Wed May 10 10:45:41 2017 -0400 +++ b/test-data/DRR015708_reverse.fastqsanger Mon Jul 03 06:30:15 2017 -0400 |
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| @@ -1,20 +1,20 @@ @HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/2 CATTANNAGNNANNNTTNNNNGANNNNNTCGANNNNNANTTTTAANCGNNNNNCTCTTNGAGAATATCAAANAGNTNAAAAATTANGCTGANNNTNGNAT -+DRR015708.1 HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938 length=100 ++ CCCFF##4<##2###32####22#####11?F#####0#07CHGI#.;#####--;BB#,;?ADDDEEDDD#,8#,#,58<?BD:#+2?@?######### @HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/2 GAAAGATGGTATTTCTGGTTTTCCAACGCGTACAGAAAGTGAGTTTGATACATTTGGAACGGGACATTCTTCTACATCTATTTCAGCAATTGTTGGGATG -+DRR015708.2 HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930 length=100 ++ BBCFFDFFHCFHHJJJJJIJJJJJJJIJJJJJJJIHGIIDHGIFIIJIIGHIIHIIJDHIIJH=DFFFFFEEEEEDEDDDEDEDDDDDCDDDCDDDBBDB @HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/2 AAATATAATTGGAGAATCAACTTTATTTTCGAATACAATTCCAAATCAAAAAGAAGATAAAACACTAGAATTATCTCAAAAGAATTCAACTCAAAAAGAT -+DRR015708.3 HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936 length=100 ++ CCCFFFFFHHHHGJIJIJJIJJJJJJJJJJJIJJJJJJJJJJJJEIJJJJHIJJIJJJIJJJIJJIJJJIJIJJJHHHGEHFFDFF>C@C>CEC;A538: @HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/2 ATTGAAACCTTTTGAGTTGATTCGTGGATTTTTGATAAATGCATAATATCCTCTAAAAATTAAGGCATAAGCATCTAACAAAAAAAGTCTTTTATCTAAT -+DRR015708.4 HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864 length=100 ++ CCCFFFFFHHHHHJEGGHIHIIJJHHJHIJIJJJGJIJJJJJJJJJJJJJIIIJIJJIJIJJIJJJJIGHEHIIHHHHFHFFEDDDDCDEEDDDDDDEDD @HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/2 TTGGTATTCTGCGGATAAATATCCTTTATCAGCTAAGAGCGTACAATTTTTAAACTGCTGTTTTATATCTTTCAGATAATGAATGTCATGCACTGAAGCT -+DRR015708.5 HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887 length=100 ++ BCCFBDFFHHHHHJJJJJJJJJJJJJJJJJJJJJIJIFIJJHHIIIJJJJGHJJJJJJJJHIIJJIJJHHHHHHGEFFFFFFCDCEEEFDDDDCDD>CDD |
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| diff -r c7620aa7e1f0 -r 1920e0508831 test-data/ERR027433_forward.fastqsanger --- a/test-data/ERR027433_forward.fastqsanger Wed May 10 10:45:41 2017 -0400 +++ b/test-data/ERR027433_forward.fastqsanger Mon Jul 03 06:30:15 2017 -0400 |
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| @@ -1,20 +1,20 @@ @IL4_4847:5:1:1051:7109/1 GCCGCCAACGTCCGACGGCGCGTCCCGCACGACTTGAACCGATCTCACCGAGACAGAACTAT -+ERR027433.1 IL4_4847:5:1:1051:7109 length=62 ++ C@CC@@@C2BBCBB:>@8@@5@>>@@@@@>@97@@==<@>>@4<'@8>:35=%&B####### @IL4_4847:5:1:1058:16093/1 AAGGTCGGGCATTCGTTCGAGCCGACGACCGCGAGGAAGCGGTTCGGCCGGGCGTAGAATCC -+ERR027433.2 IL4_4847:5:1:1058:16093 length=62 ++ ?ABBABB;<@>@=<?@CBBB:@2>BCBB,,?):7@/3$54'818->1-+=+()$6--C8+?1 @IL4_4847:5:1:1111:15034/1 TCGATCCGCAGGGCAATCTGTGGATCCCGGCGTTCGACGACGGCGGGCGGGTGGCTCGGCAT -+ERR027433.3 IL4_4847:5:1:1111:15034 length=62 ++ 2524;@@@/4<@6@;9?C@@93@>BAB2>>C@>B>C4BC4@-+B<@525++%=)######## @IL4_4847:5:1:1122:6048/1 ATCTCCTCGACGCGCACCAGATAGCGGTCGTAGCAATCGCCGTCCACGCCGACGGGCCCACT -+ERR027433.4 IL4_4847:5:1:1122:6048 length=62 ++ BBB@@@@@@@AB.<@2)7;B-@==:@>@@@A7@<AA4:A3'@9+4;&00'9+AC5--DA5,? @IL4_4847:5:1:1138:20693/1 CTGCTCGCGCGAGAACGCGCGCAAGCTCGGGGGCGGTGGCGGGGTCGGGCGACACCGATGTA -+ERR027433.5 IL4_4847:5:1:1138:20693 length=62 ++ CB<C7@>);9@@@@=1B@@@@2@=*:4@@@0%(-$,'3%%'%$%$,44%3&$=$C;CC-C## |
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| diff -r c7620aa7e1f0 -r 1920e0508831 test-data/ERR027433_reverse.fastqsanger --- a/test-data/ERR027433_reverse.fastqsanger Wed May 10 10:45:41 2017 -0400 +++ b/test-data/ERR027433_reverse.fastqsanger Mon Jul 03 06:30:15 2017 -0400 |
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| @@ -1,20 +1,20 @@ @IL4_4847:5:1:1051:7109/3 AACGCACTGCGCGCGGACTCGCCCCCGCGGCCACTCCGTGGGCCGGCGTACGGA -+ERR027433.1 IL4_4847:5:1:1051:7109 length=54 ++ )(664;(>>/:1<+/'())0)',8%'*7'+9904)'(+()'''':+4+'.7)'( @IL4_4847:5:1:1058:16093/3 GCATAGCTGCCCTCGCCTTCTACTCGCACCGAACAAGCGGCCCGCCTACGCGGG -+ERR027433.2 IL4_4847:5:1:1058:16093 length=54 ++ ;=>1(/2(:/=@(:'9/<(*'&.(?.6)(';+.5''-3.&''7(96%0:+($2$ @IL4_4847:5:1:1111:15034/3 GAGTGGAGCCGCGGACGGGAGCGCGGCGGCTGCCTCACAGCACCCGGGGGGTCG -+ERR027433.3 IL4_4847:5:1:1111:15034 length=54 ++ ::3+:2655(*('((3*&&&4+')6'3/2,+++*.+')-/)4((<-+&&'&%<( @IL4_4847:5:1:1122:6048/3 GAGGTCGGCGTTCTGGATGACAGGCGCGAAGCCCCCGCCGTCGGTGCCTTCACG -+ERR027433.4 IL4_4847:5:1:1122:6048 length=54 ++ =8+(-(,(3.5*=99+;).)8'(,(/(+(-6@'-3<6&,%/4++)')1/)>(.& @IL4_4847:5:1:1138:20693/3 TGGACGTTGTGGTGGTTGTAAGAGATTTCGCTCCCCATGTTGGCGAGCTGCGAT -+ERR027433.5 IL4_4847:5:1:1138:20693 length=54 ++ ;)?5;=9996@((((097:41=,A((+)5>9,:''''67+9)=(968-(8;8)3 |
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| diff -r c7620aa7e1f0 -r 1920e0508831 test-data/SRR1993644.fastqsanger --- a/test-data/SRR1993644.fastqsanger Wed May 10 10:45:41 2017 -0400 +++ b/test-data/SRR1993644.fastqsanger Mon Jul 03 06:30:15 2017 -0400 |
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| @@ -1,20 +1,20 @@ @1/2 TATACTACTGTCATGTTTGCTTTTTTCGTGCTCATTACCTTATCGTATGCTTCCATCCAAAGATCTAGTTGTTTATAATATTCTCCCGGCCTTACTTCAAC -+SRR1993644.1 1 length=101 ++ ?@<DDDADDFAAC@>GG<FDCBHIIGB:8??DEAHGAFEDF<B?F9DBFFCDHF>48BBCF)8877=@=@C7=E??EBD:AADA;>C3;BB6:A@>>@:3> @2/2 AAAAAAACTTTCTTTACAGGCGTAAAGAAAGTGAAATTGACAGTATTTATACATGAAATAGCAATGTCTTTCCCACTTCCCTACGCTGGCATTAACCAGAT -+SRR1993644.2 2 length=101 ++ <@@DA6DDF42ABGF9F?F@C<EDDDFBGI>04BGC>BFF><?*88BDFDEAFFDGCGEFEEFIFFFEF>EBDBB@@:ACCCAB8@?=;B<@BABBBBB?# @3/2 GTGCCATCATTTTCTATCCATTATTATGGATTATTGGCTCATCGTTTAATCCGGGTGATAGTTTATCTGGATCAAGTATTATTCCACAAAATGCAACGTTA -+SRR1993644.3 3 length=101 ++ =BBFFFFFHHHHHJJJJJJJJJJJJIJIJEIIGIJJJHGIGGIIGHIDIJGHIIJ?FFHGIIJJJJJJJJHGIHHHCEHFFFFFFFFEAECCDADDDDDDD @4/2 TTCAAAACACATAAAGCTAATTGCCGCATATGACAATATTGCTAAAATAATTTTTTTACCAGATATCGGTGTTAATCGAAATAATGTACTTTCGGTCATTT -+SRR1993644.4 4 length=101 ++ BBCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJIIJJJJJJJIJJHHHHHFFDDCDEEEDDDDDDDDEDDDFFFEDDDDDDDDE @5/2 ACTTGCCAATGCGATGCACCAATCTTTTCAGCAATAATCGGCAAAATTGGGTCGACTACTCCTATACCTGAAAAGGCAAGGAAAGTAGCCAACACTGTAAT -+SRR1993644.5 5 length=101 ++ BCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHIIJIJHHHHFFFFFFEEEEEEDDDDDDDDDDDDDCDDDDDDDDDDDDDED |
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| diff -r c7620aa7e1f0 -r 1920e0508831 test-data/fastq_dump_result.fastq --- a/test-data/fastq_dump_result.fastq Wed May 10 10:45:41 2017 -0400 +++ b/test-data/fastq_dump_result.fastq Mon Jul 03 06:30:15 2017 -0400 |
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| @@ -1,40 +1,40 @@ @1/1 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT -+SRR925743.1 1 length=100 ++ EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<EDDE?2@?AEEDEED=D+C?5@A=6:>BA8:>@:4+36945&4354445>/B>@ @1/2 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA -+SRR925743.1 1 length=100 ++ GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF?EHGGHHHGHFHEHDEHGHFFEEE9BDDBEBAD.AD:ACBBC=4@>?5>=+? @2/1 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGT -+SRR925743.2 2 length=100 ++ HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFGGEEAEEEDD0ADDBD9BDBDDA@6?BA;?CD=:-7<<::)1;5,6-6A@?=9 @2/2 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA -+SRR925743.2 2 length=100 ++ HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHHHHHHHHHHGHHHGHHBHGHHFDBDDED5FCFCEEGF<@>>>@,<5<@@?>;D @3/1 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCA -+SRR925743.3 3 length=100 ++ HHHHFHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHGEFHGEGGFGGGGGGHHHHEFEIDDEEEEEDD4DD;??:6>6<@.<==@?.@@<?##### @3/2 ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT -+SRR925743.3 3 length=100 ++ HHHHHHHHHFIEGFHFHDHHHHGFFHGEGDIGGEGGHHHAGEGGGDHHHHHHHHHHHFGDGGGEGDFFF>BEEEE3B;BB;>B7C@DA=DFBDD.BEE=9 @4/1 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTA -+SRR925743.4 4 length=100 ++ HHGBHHHHGFHHHHHFDHHFHGEHHHHHEFHHHHEGEGEFFFAFFFDCFGF?@GCDFGFEFHHEFDF*F6DC4DD:A8>@D@CD8->=>=<@CB@##### @4/2 ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT -+SRR925743.4 4 length=100 ++ GFFFHHFFHHHFHHFEFGGBGEEEE?<9?6=>>:=DDDD@DBGDB;DBDBA.ADD8<2<>6A@=A5>550=>>>>BE;EEEDEEE79+336<68=BCEB@ @5/1 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTCACACTCACCCTA -+SRR925743.5 5 length=100 ++ GGGFGFFGGGFBGGEGGFFGGGCFFGGGGGEGFFFFFGFFGFFFDFFB+FGGFEE?FCF::7B5A?+BB############################### @5/2 ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGTTAGGGGTAGGGT -+SRR925743.5 5 length=100 ++ 479<.>><:<A7BABBE8@=:<<:@BB?C75:2?;.5<<3FEFGEEC88FEDEE=AB><AA@B<ABDC8.27<9:58.58??6<:@>+?=9@######## |
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| diff -r c7620aa7e1f0 -r 1920e0508831 test-data/fastq_dump_result.fastq.gz |
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| Binary file test-data/fastq_dump_result.fastq.gz has changed |