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changeset 8:1920e0508831 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 39ca11da7daeb3fa030fcb28e8987f8d7f24aec3
author iuc
date Mon, 03 Jul 2017 06:30:15 -0400
parents c7620aa7e1f0
children 6c60903f70ac
files 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
diffstat 8 files changed, 37 insertions(+), 36 deletions(-) [+]
line wrap: on
line diff
--- 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":
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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##
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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@########
Binary file test-data/fastq_dump_result.fastq.gz has changed