Mercurial > repos > iuc > sra_tools
changeset 40:8848455c0270 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 7632986831e24fcd189a57d824b9e6b1d5dc5c4c
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--- a/fasterq_dump.xml Mon Jun 03 15:07:36 2024 +0000 +++ b/fasterq_dump.xml Mon Aug 26 14:59:28 2024 +0000 @@ -73,7 +73,7 @@ <inputs> <expand macro="input_conditional"/> <section name="adv" title="Advanced Options" expanded="False"> - <expand macro="defline" defline_param="--seq-defline" defline_default="@$sn/$ri"/> + <expand macro="defline" defline_param="--seq-defline" defline_default="@$ac.$sn/$ri"/> <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--min-read-len"/> <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end)."> <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option>
--- a/fastq_dump.xml Mon Jun 03 15:07:36 2024 +0000 +++ b/fastq_dump.xml Mon Aug 26 14:59:28 2024 +0000 @@ -91,7 +91,7 @@ <option value="fastqsanger.bz2">bzip2 compressed fastq</option> </param> <section name="adv" title="Advanced Options" expanded="False"> - <expand macro="defline" defline_param="--defline-seq" defline_default="@$sn[_$rn]/$ri"/> + <expand macro="defline" defline_param="--defline-seq" defline_default="@$ac.$sn[_$rn]/$ri"/> <param name="minID" type="integer" label="Minimum spot ID" optional="true" help="Minimum spot id to be dumped." argument="--minSpotId"/> <param name="maxID" type="integer" label="Maximum spot ID" optional="true" help="Maximum spot id to be dumped." argument="--maxSpotId"/> <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--minReadLen"/> @@ -279,8 +279,8 @@ </section> <output_collection name="list_paired" type="list:paired" count="1"> <element name="SRR522874.sra"> - <element name="forward" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> - <element name="reverse" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> + <element name="forward" file="SRR522874.sra_2_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> + <element name="reverse" file="SRR522874.sra_4_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> </element> </output_collection> </test>
--- a/macros.xml Mon Jun 03 15:07:36 2024 +0000 +++ b/macros.xml Mon Aug 26 14:59:28 2024 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.1.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">22.01</token> <xml name="edam_ontology"> <edam_topics>
--- a/test-data/DRR015708_forward.fastqsanger Mon Jun 03 15:07:36 2024 +0000 +++ b/test-data/DRR015708_forward.fastqsanger Mon Aug 26 14:59:28 2024 +0000 @@ -1,20 +1,20 @@ -@HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/1 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/1 NTATTGTAGCGCACTATGAGGTCGCTCATTANTNTACATCNNCATCCAAATTTCAGCATNANTTTNNNNNTGTTTGATATTCTCAAAGNGATNAACGTTT + #1=DDFFFHGHHHJIIIIGIJFHIJJJJJJI#0#08DFII##-7@FHIIJJJJGEHEEE#,#,,;#####,,;?DCCDEFEEFCDDDD#+2+#+2<?<CC -@HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/1 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/1 NTTCTAAACTCATTCCAGAAGTAATTGATGCGTCACCAATAATTGCAATATGTTTTCTATTGATTTGATTGATTTTATCTGCTGTTGCCATCCCAACAAT + #4=DDFFFHHHHHJJJJJJIIHIJJJJJJJJIHJJJJJIJJJJJJJJJJJJJIJJJJJJJJJJJJJJIIIICHHGEHHGIFEHHHHFFDFFFDDCEB@AC -@HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/1 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/1 NTCACCTACAACTCGAATATTCGAATGATATGTGATATTGTTAGATGATTTTGGCATGCTTGCAGAAAGTGCATAAACACCTGTATTGATTCCCGAATTT + #4=DFFFFHHHHHIJIJJIHIIJIIJJJJIJIHIIGGIIJHIEHGGHGHIIJJJIIJJJJJHHCHGGGE@FHGHIIJIEHHEDCCDCCDEEED@AB/=A# -@HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/1 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/1 NCTTAAAACTTATTAAATGAATCAATTAGATAAAAGACTTTTTTTGTTAGATGCTTATGCCTTAATTTTTAGAGGATATTATGCATTTATCAAAAATCCA + #4=DFFFFHHHHHJJJIJJJJJJJJJJJJJJJJIHGDGHIJJJJJJGHHJGIJIJJJJJJJIJIJJJJJHFFHGFDDFEEFEECCEEDEEDDCC3<A5>C -@HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/1 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/1 NTAAAGGTTATTGTGCTTCACAGAAAATGCATTATTATGGGTATAAACTTCATGCGGTTTGCTCAGCGGAAGGTGTCTTTCAAAGTTTGGATATTAGTCC + #1=DDFFEHHHHHGIJJJJGIJJJJJJJJJJJJIJJJJJJJCFGFIIHJIJHIJJJJHIJJJJIJIJIFHBDE;@ACEEEDDCCCCCDDDCCDCCFECCC
--- a/test-data/DRR015708_reverse.fastqsanger Mon Jun 03 15:07:36 2024 +0000 +++ b/test-data/DRR015708_reverse.fastqsanger Mon Aug 26 14:59:28 2024 +0000 @@ -1,20 +1,20 @@ -@HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/2 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/2 CATTANNAGNNANNNTTNNNNGANNNNNTCGANNNNNANTTTTAANCGNNNNNCTCTTNGAGAATATCAAANAGNTNAAAAATTANGCTGANNNTNGNAT + CCCFF##4<##2###32####22#####11?F#####0#07CHGI#.;#####--;BB#,;?ADDDEEDDD#,8#,#,58<?BD:#+2?@?######### -@HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/2 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/2 GAAAGATGGTATTTCTGGTTTTCCAACGCGTACAGAAAGTGAGTTTGATACATTTGGAACGGGACATTCTTCTACATCTATTTCAGCAATTGTTGGGATG + BBCFFDFFHCFHHJJJJJIJJJJJJJIJJJJJJJIHGIIDHGIFIIJIIGHIIHIIJDHIIJH=DFFFFFEEEEEDEDDDEDEDDDDDCDDDCDDDBBDB -@HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/2 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/2 AAATATAATTGGAGAATCAACTTTATTTTCGAATACAATTCCAAATCAAAAAGAAGATAAAACACTAGAATTATCTCAAAAGAATTCAACTCAAAAAGAT + CCCFFFFFHHHHGJIJIJJIJJJJJJJJJJJIJJJJJJJJJJJJEIJJJJHIJJIJJJIJJJIJJIJJJIJIJJJHHHGEHFFDFF>C@C>CEC;A538: -@HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/2 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/2 ATTGAAACCTTTTGAGTTGATTCGTGGATTTTTGATAAATGCATAATATCCTCTAAAAATTAAGGCATAAGCATCTAACAAAAAAAGTCTTTTATCTAAT + CCCFFFFFHHHHHJEGGHIHIIJJHHJHIJIJJJGJIJJJJJJJJJJJJJIIIJIJJIJIJJIJJJJIGHEHIIHHHHFHFFEDDDDCDEEDDDDDDEDD -@HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/2 +@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/2 TTGGTATTCTGCGGATAAATATCCTTTATCAGCTAAGAGCGTACAATTTTTAAACTGCTGTTTTATATCTTTCAGATAATGAATGTCATGCACTGAAGCT + BCCFBDFFHHHHHJJJJJJJJJJJJJJJJJJJJJIJIFIJJHHIIIJJJJGHJJJJJJJJHIIJJIJJHHHHHHGEFFFFFFCDCEEEFDDDDCDD>CDD
--- a/test-data/ERR027433_forward.fastqsanger Mon Jun 03 15:07:36 2024 +0000 +++ b/test-data/ERR027433_forward.fastqsanger Mon Aug 26 14:59:28 2024 +0000 @@ -1,20 +1,20 @@ -@IL4_4847:5:1:1051:7109/1 +@ERR027433.IL4_4847:5:1:1051:7109/1 GCCGCCAACGTCCGACGGCGCGTCCCGCACGACTTGAACCGATCTCACCGAGACAGAACTAT + C@CC@@@C2BBCBB:>@8@@5@>>@@@@@>@97@@==<@>>@4<'@8>:35=%&B####### -@IL4_4847:5:1:1058:16093/1 +@ERR027433.IL4_4847:5:1:1058:16093/1 AAGGTCGGGCATTCGTTCGAGCCGACGACCGCGAGGAAGCGGTTCGGCCGGGCGTAGAATCC + ?ABBABB;<@>@=<?@CBBB:@2>BCBB,,?):7@/3$54'818->1-+=+()$6--C8+?1 -@IL4_4847:5:1:1111:15034/1 +@ERR027433.IL4_4847:5:1:1111:15034/1 TCGATCCGCAGGGCAATCTGTGGATCCCGGCGTTCGACGACGGCGGGCGGGTGGCTCGGCAT + 2524;@@@/4<@6@;9?C@@93@>BAB2>>C@>B>C4BC4@-+B<@525++%=)######## -@IL4_4847:5:1:1122:6048/1 +@ERR027433.IL4_4847:5:1:1122:6048/1 ATCTCCTCGACGCGCACCAGATAGCGGTCGTAGCAATCGCCGTCCACGCCGACGGGCCCACT + BBB@@@@@@@AB.<@2)7;B-@==:@>@@@A7@<AA4:A3'@9+4;&00'9+AC5--DA5,? -@IL4_4847:5:1:1138:20693/1 +@ERR027433.IL4_4847:5:1:1138:20693/1 CTGCTCGCGCGAGAACGCGCGCAAGCTCGGGGGCGGTGGCGGGGTCGGGCGACACCGATGTA + CB<C7@>);9@@@@=1B@@@@2@=*:4@@@0%(-$,'3%%'%$%$,44%3&$=$C;CC-C##
--- a/test-data/ERR027433_reverse.fastqsanger Mon Jun 03 15:07:36 2024 +0000 +++ b/test-data/ERR027433_reverse.fastqsanger Mon Aug 26 14:59:28 2024 +0000 @@ -1,20 +1,20 @@ -@IL4_4847:5:1:1051:7109/3 +@ERR027433.IL4_4847:5:1:1051:7109/3 AACGCACTGCGCGCGGACTCGCCCCCGCGGCCACTCCGTGGGCCGGCGTACGGA + )(664;(>>/:1<+/'())0)',8%'*7'+9904)'(+()'''':+4+'.7)'( -@IL4_4847:5:1:1058:16093/3 +@ERR027433.IL4_4847:5:1:1058:16093/3 GCATAGCTGCCCTCGCCTTCTACTCGCACCGAACAAGCGGCCCGCCTACGCGGG + ;=>1(/2(:/=@(:'9/<(*'&.(?.6)(';+.5''-3.&''7(96%0:+($2$ -@IL4_4847:5:1:1111:15034/3 +@ERR027433.IL4_4847:5:1:1111:15034/3 GAGTGGAGCCGCGGACGGGAGCGCGGCGGCTGCCTCACAGCACCCGGGGGGTCG + ::3+:2655(*('((3*&&&4+')6'3/2,+++*.+')-/)4((<-+&&'&%<( -@IL4_4847:5:1:1122:6048/3 +@ERR027433.IL4_4847:5:1:1122:6048/3 GAGGTCGGCGTTCTGGATGACAGGCGCGAAGCCCCCGCCGTCGGTGCCTTCACG + =8+(-(,(3.5*=99+;).)8'(,(/(+(-6@'-3<6&,%/4++)')1/)>(.& -@IL4_4847:5:1:1138:20693/3 +@ERR027433.IL4_4847:5:1:1138:20693/3 TGGACGTTGTGGTGGTTGTAAGAGATTTCGCTCCCCATGTTGGCGAGCTGCGAT + ;)?5;=9996@((((097:41=,A((+)5>9,:''''67+9)=(968-(8;8)3
--- a/test-data/SRR1993644.fastqsanger Mon Jun 03 15:07:36 2024 +0000 +++ b/test-data/SRR1993644.fastqsanger Mon Aug 26 14:59:28 2024 +0000 @@ -1,20 +1,20 @@ -@1/2 +@SRR1993644.1/2 TATACTACTGTCATGTTTGCTTTTTTCGTGCTCATTACCTTATCGTATGCTTCCATCCAAAGATCTAGTTGTTTATAATATTCTCCCGGCCTTACTTCAAC + ?@<DDDADDFAAC@>GG<FDCBHIIGB:8??DEAHGAFEDF<B?F9DBFFCDHF>48BBCF)8877=@=@C7=E??EBD:AADA;>C3;BB6:A@>>@:3> -@2/2 +@SRR1993644.2/2 AAAAAAACTTTCTTTACAGGCGTAAAGAAAGTGAAATTGACAGTATTTATACATGAAATAGCAATGTCTTTCCCACTTCCCTACGCTGGCATTAACCAGAT + <@@DA6DDF42ABGF9F?F@C<EDDDFBGI>04BGC>BFF><?*88BDFDEAFFDGCGEFEEFIFFFEF>EBDBB@@:ACCCAB8@?=;B<@BABBBBB?# -@3/2 +@SRR1993644.3/2 GTGCCATCATTTTCTATCCATTATTATGGATTATTGGCTCATCGTTTAATCCGGGTGATAGTTTATCTGGATCAAGTATTATTCCACAAAATGCAACGTTA + =BBFFFFFHHHHHJJJJJJJJJJJJIJIJEIIGIJJJHGIGGIIGHIDIJGHIIJ?FFHGIIJJJJJJJJHGIHHHCEHFFFFFFFFEAECCDADDDDDDD -@4/2 +@SRR1993644.4/2 TTCAAAACACATAAAGCTAATTGCCGCATATGACAATATTGCTAAAATAATTTTTTTACCAGATATCGGTGTTAATCGAAATAATGTACTTTCGGTCATTT + BBCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJIIJJJJJJJIJJHHHHHFFDDCDEEEDDDDDDDDEDDDFFFEDDDDDDDDE -@5/2 +@SRR1993644.5/2 ACTTGCCAATGCGATGCACCAATCTTTTCAGCAATAATCGGCAAAATTGGGTCGACTACTCCTATACCTGAAAAGGCAAGGAAAGTAGCCAACACTGTAAT + BCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHIIJIJHHHHFFFFFFEEEEEEDDDDDDDDDDDDDCDDDDDDDDDDDDDED
--- a/test-data/SRR925743_forward.fastqsanger Mon Jun 03 15:07:36 2024 +0000 +++ b/test-data/SRR925743_forward.fastqsanger Mon Aug 26 14:59:28 2024 +0000 @@ -1,20 +1,20 @@ -@1/1 +@SRR925743.1/1 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT + EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<EDDE?2@?AEEDEED=D+C?5@A=6:>BA8:>@:4+36945&4354445>/B>@ -@2/1 +@SRR925743.2/1 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGT + HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFGGEEAEEEDD0ADDBD9BDBDDA@6?BA;?CD=:-7<<::)1;5,6-6A@?=9 -@3/1 +@SRR925743.3/1 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCA + HHHHFHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHGEFHGEGGFGGGGGGHHHHEFEIDDEEEEEDD4DD;??:6>6<@.<==@?.@@<?##### -@4/1 +@SRR925743.4/1 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTA + HHGBHHHHGFHHHHHFDHHFHGEHHHHHEFHHHHEGEGEFFFAFFFDCFGF?@GCDFGFEFHHEFDF*F6DC4DD:A8>@D@CD8->=>=<@CB@##### -@5/1 +@SRR925743.5/1 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTCACACTCACCCTA + GGGFGFFGGGFBGGEGGFFGGGCFFGGGGGEGFFFFFGFFGFFFDFFB+FGGFEE?FCF::7B5A?+BB###############################
--- a/test-data/SRR925743_reverse.fastqsanger Mon Jun 03 15:07:36 2024 +0000 +++ b/test-data/SRR925743_reverse.fastqsanger Mon Aug 26 14:59:28 2024 +0000 @@ -1,20 +1,20 @@ -@1/2 +@SRR925743.1/2 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA + GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF?EHGGHHHGHFHEHDEHGHFFEEE9BDDBEBAD.AD:ACBBC=4@>?5>=+? -@2/2 +@SRR925743.2/2 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA + HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHHHHHHHHHHGHHHGHHBHGHHFDBDDED5FCFCEEGF<@>>>@,<5<@@?>;D -@3/2 +@SRR925743.3/2 ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT + HHHHHHHHHFIEGFHFHDHHHHGFFHGEGDIGGEGGHHHAGEGGGDHHHHHHHHHHHFGDGGGEGDFFF>BEEEE3B;BB;>B7C@DA=DFBDD.BEE=9 -@4/2 +@SRR925743.4/2 ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT + GFFFHHFFHHHFHHFEFGGBGEEEE?<9?6=>>:=DDDD@DBGDB;DBDBA.ADD8<2<>6A@=A5>550=>>>>BE;EEEDEEE79+336<68=BCEB@ -@5/2 +@SRR925743.5/2 ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGTTAGGGGTAGGGT + 479<.>><:<A7BABBE8@=:<<:@BB?C75:2?;.5<<3FEFGEEC88FEDEE=AB><AA@B<ABDC8.27<9:58.58??6<:@>+?=9@########