| Next changeset 1:5ceeb5a5d70f (2021-10-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84" |
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added:
artic_guppyplex.xml macros.xml test-data/SRR11410539_seqtk_sample_500_1.fastq test-data/SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta test-data/all_fasta.loc test-data/gupplyplex_output.fastq test-data/nCoV-2019.V1.bed test-data/nCoV-2019.reference.fasta test-data/nCoV-2019.scheme.V1.bed test-data/nCoV-2019.scheme.V3.bed test-data/primer_scheme_bedfiles.loc test-data/test.fastq tool-data/all_fasta.loc.sample tool-data/primer_scheme_bedfiles.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 7a82006f7c05 artic_guppyplex.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/artic_guppyplex.xml Fri Aug 27 20:34:52 2021 +0000 |
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| @@ -0,0 +1,50 @@ +<tool id="artic_guppyplex" name="ARTIC guppyplex" version="@PACKAGE_VERSION@+galaxy0" profile="20.09"> + <description>Filter Nanopore reads by read length and (optionally) quality</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@PACKAGE_VERSION@">artic</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + mkdir inputs && + #for $i, $elem in enumerate($input) + ln -fs '$elem' inputs/fastq${i}.fastq && + #end for + artic guppyplex --min-length $min_length --max-length $max_length + --directory inputs/ + --prefix artic_guppyplex --output '$output1' + ]]> + </command> + <inputs> + <param name="input" multiple="true" type="data" format="fastq" label="Nanopore reads (FASTQ format" /> + <param name="max_length" type="integer" label="Remove reads longer than" value="700" help="remove reads greater than this number of base pairs" /> + <param name="min_length" type="integer" label="Remove reads shorter than" value="400" help="remove reads less than this number of base pairs" /> + <param name="skip_quality_check" argument="--skip-quality-check" type="boolean" truevalue="--skip-quality-check" falsevalue="" checked="False" label="Do not filter on quality score (speeds up processing)" /> + </inputs> + <outputs> + <data name="output1" format="fastq" from_work_dir="run_name_.fastq" /> + </outputs> + <tests> + <test> + <param name="input" value="test.fastq" /> + <output name="output1" file="gupplyplex_output.fastq"/> + </test> + </tests> + <help><![CDATA[ + The ARTIC_ guppyplex tool filters reads by length and (optionally) quality. + This filter is typically used as a pre-processing step in the processing + of amplicon sequencing Nanopore reads, where a size-based filter can + be used to remove possibly-chimeric reads. + + The default paramters of the tool (minimum length of 400 and maximum of 700) + are based on the ARTIC amplicon scheme. If used with a different amplicon + scheme they should be adjusted to use the minimum length of an amplicon as + the minimum length and the maximum length of an amplicon plus 200 as the + maximum length. + + .. _ARTIC: https://artic.readthedocs.io/en/latest/ + ]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 7a82006f7c05 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Aug 27 20:34:52 2021 +0000 |
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| @@ -0,0 +1,18 @@ +<macros> + <token name="@PACKAGE_VERSION@">1.2.1</token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{githubartic-ncov2019, + author = {Nick Loman and the ZiBRA Project and the ARTIC project}, + year = {2017}, + title = {ARTIC toolkit}, + publisher = {GitHub}, + journal = {GitHub repository}, + howpublished{\url{https://github.com/artic-network/fieldbioinformatics}}, + } + </citation> + <yield /> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 7a82006f7c05 test-data/SRR11410539_seqtk_sample_500_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SRR11410539_seqtk_sample_500_1.fastq Fri Aug 27 20:34:52 2021 +0000 |
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| b'@@ -0,0 +1,2000 @@\n+@SRR11410539.882919 882919/1\n+CTTGGGCATTAGTCGTTCAGTTACATGTACTAAGGTTAAACAGACGACTACAAACGGAATCCCGACAGCACCTACCAATAACTTTCAAATCGTAGTCTGTTCTCTAAATATGAACTTTAAAATCTGTGTGGCTGTCATCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCATCTTCTGCAGGCTGCTTACGGTTCGTCCGTGTTGCAGCCGATCCTCTTTATCTAGGTTTGTCGGGTGTGACCGAAGGTAAGATGGAGAGCCTTGTCCCCTGGTTTCAACGAGAAAACACGTCCAGTTTGCCTGTTTTACAGGTTCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGAGTCTTATCAGAGCACGTCAACATCTTAAAGATGAGGGTGCTATTGGTTTTCCCGTTTGTAGTCGTCTGTTTAACCTTAGCAATACGTAACTTT\n++\n+$0%#%$##\'*(&)&&*)0/09711$$$&&/3%%)*3;:<:99:;;992&6;DF;<$&,2%%6/8:64=D@B?>:37//.11%%%%\'#%--($&%&)077AB:6A4/0.)\'(+.223301344/3%\'(*0169<,(3%\'\'$%%,+5//,((,40=,8%$8@>?=/&&15676.0++)1335:<:?<;>9;>=A??6**5<830-%&)4//265/1\'59:H@=>3//8:53/-13AE8<A:<:9:?977#%\'\'&&++.0&&)%$%&\'*12/05;ABC<4F)/AAAA?=99450*>;;=?B??B@/)+42.28122+*2/4//)<126,,.2,<9:,83$$-&9@<=6;<DA<<H4@@=CCAA3038)%%\'74.30+(/++*,.3010-7@A7<@C895.\'0:>@>54800+8=<70/6)*>9;EJBDE@0:24&\'(4<::3)).,.,/1,&,&*,0C=@<=9?;7>>;77*+,)-),%&*//;>B?<72&\'+*\n+@SRR11410539.1188960 1188960/1\n+TATTACTACCATTCGTTCCCATGCCTTACTAAGGTCACTCGACCAACTCTGGCATGAATCGACAGCACGCGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAGCTTTTGGCAATCATCTGGATGCACCCACACCACTAGGCATTGATTTAGATAGTGGAGTATGGCTACATACTACTTGTTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTTTACCCTCAGATGAGGATGAAGAAGGTGATTGTGAAGAGAAGTTTGAGCCATCAAACTCAATATGAGTATGTAGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCGCACTTCTGCATCTTCAACTGAAGAGCAAGAAGAAGATTGGTTAGATCGAAGGTGCTGTCAATTCCGTTTGTAGTAATCTGTTTAACCTTAGCAATACGTAACTT\n++\n+#$#$$#$$%%%%\'%&$$%)(%%###$%($%))(\'(\'%"$%#$#%#%"\'-$"##$&%&*&086)%421$$*%&).6./8<ACFELGBBCACC>;:B@>D2:BF@21&+/?@C=80.B<<B?:<:9=<614)9844<?BABF93;11234\'/003+&\'*()%#&.9+)+)0%%(***/1632.&&&13>=><1./15-101\'*914,6=;?<=>:-.52261+((*\'-065280,-.;-58@32?EDA8923<0:552:8;602<;03+.<:=:?3/0(1>?<(780@/4)<?=2\'&8,,((2.)\'\'+-,&$5,+$&\'\'-22111<;4-:9:09-7((.-)&*,10%%$%*.&%167B@@EIFMD=79./40459::BA@=*/*0058&&,$$%029;:76\'$#//=9://1(++69;36=:\'0-,3)4//558=>--.%&&&-).<0.5&))&($\'%5499<+&+$$%%.64<9;?970((+</89994@:;00%%(\n+@SRR11410539.1794060 1794060/1\n+CATTTATTGCTTCGTTCAGTTACGTATTGCTAAGGTTAAACAGACGACTACAAACGGAATCGACAGCACCTAGCAGCATCTACAGCAAAAGCACAGAAAGATAATACAGTTGAATTGGCAGGCACTTCTGTTTGCATTACCAGCTTGTGAACGATGCTGTGGCAGCTAAACTACCAAGTACCATACCTCTATTTAGGTTGTTTTAATCCTTTAATAAAGTATAAATACTTCACTTTAGGACCTTTAGGTGTGTCTGTAACAAACCTACAAGGTGGTTTGATTCTGTATAGATAGTACCAGTTCCATCACTCTTAGGGAATCTGGCCATTTCAAATCATTAAATCGGATAACAGGCACAAGTACAAACCTACCTCCCTTTTGTTGTGTTGTAGTAAGCTAACGCATTGTCATCAGTGCAAGCAGTTTGTGTAGTACCGGCAGCACAAAGACATCTGTCGTAAGGTGCTGTCGATTCCGTTTAATAGTCGTCTGTTTAACCTTAGCAATACGTAACT\n++\n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n+@SRR11410539.635976 635976/1\n+GTTGTACTTCGTTCGTTACGTATTGCTAAGGTTAAACAGACGACTACAAACAGATCGACAGCACCTCATGGCTGCATCACGGTCAAATTCAGATTGCCACATTCAAGACTTCTTCAACTTTTTAAGAACAACCAGAATCACCATTAGCAACAGCCTGCTCATAAGCTTCTTGAGCAGTAGCAAAAACTGCATATGATGGAAGGGAACTAAACTCTGAGGCTATAGCTTGTAAGGTTGCCCTGTTGTCCAGCATTTCTTCACAAAGCTTGTTTATGTCTACAGCACCCTGCATGGAAAGCAAAACAGAAAGTAGTGAAACCATTTTTCAGGCTTCAGTAGTATCTTTAGCTAAGGAATGTCATTGTGTAACTGGACACATTGAGCCCACAATTTAGATGATGATTCTACTCTGAGTTGTTGCAAAACTGAGAGTAAGACTACTGATGTGCAAGGTGCTGTCGATTCCGTTGTAGTCGTCTGTTTAACCTTAGCAATACGTAAC\n++\n+*$%)35;=@;=H<,*1)9?@EI>I=@?\'(5>IHEG93/3/6.+&%#$.269--<9=8:56168==FD>?,232,&%\'*.2056<9:8:2+%1+2/\'25:?@@:8-.--"#&/26F<?DVTSNB,,(9B?9)$*?767;AD@?99=9<>>?BI>B?A?A8C43/1&()+9HGDD89784447?>>9\'3\'+DB@CADB?;=,4,;A;A>?;<-?=<9<-4:4:>3-/&&)*8893>GF;93+8>67@))@B;C>?AC@C04,,-.\'$$$0:>@CB;@>BC?@>GFEHI@;68:44546>?=AAHI@55=5=><34>@A:==@@>B'..b'CGCCTCCTCCATGTTTAAGGTAAACATTGGCTGCATTAACAACCACTGTTGGTTTTACCTTTTAGCTTCTTCCATAATGTCTGCATTTTTAATGTATACATTGTCAGTAAGTTTTTAAATAACCACTAAAACTATTCACTTCAATAGTCTGAATAACTGGTAGTTCCATCTCTAATTGAGGTTGAACCTCAACAATTATTGAATAGTAGTTGCATCTGATTGTCCTCTGCCGTCTTGTTGACCAACAGTTTGTTGACTATCATCATCTAACCAATCTTCTTCTTGCTCTTCTTCAGGTTGAGCGAAGTGGCACAATTAGGTGCTGTCGGTCCGTTTGTAGTCGTCCTGTTTAACCTTGGCAATACGTAAC\n++\n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n+@SRR11410539.817445 817445/1\n+CATTGTACTTCGTTCAGTTACGTATTGCTGGGTTAAACGGGCGACTACAAACAAGTCGACACAGCACCGCCCGGTTGAGTGTTGTCAATGCCAGATACGTGCTAAGCATATATTACGGTAACGACCCTGCTGCGCATCAGTTACCTCTTTGCTGTTGCTAGCTAAAGGACACACTGGAACCAGAATATTTCAGTTCGGTGTGAACTTATGAAAACTATGATCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATGTTGACACTGTAGCGTGCTTTGGTTTATGATAATAAACAACACATAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCACAAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAGAGGTGCTGTCGATTCCGTTTGCCGGTCATCTGTTTAACCTTAGCAATACATAAC\n++\n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n+@SRR11410539.1565287 1565287/1\n+CGGTATGCTTCGTTCAGTTACGTATTGCTAAGGTTAAACAGACGACTACAAACGGAATCGACACTTCCTTCCCATCTGGTAAAGTTGAGGTTTGTATGGTACAAGTAACTTGTGGTACAACTACGCTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTTAAGCTTAAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAGTTTGTTCGCATTCAACCTTAGGACAGACTTTTTCAGTGTTAACTTGTTACAATGGTTCACCATCTGGTGTTTACCAATGTGCTATGAGGCCCAATTTCACTAGGTGCTGTCGGTCCGTTTTGACGGCTCGTCTGTTTAACCTTAGCAATACGTAAC\n++\n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n+@SRR11410539.1083900 1083900/1\n+GTTATTCGTTCAGTTACGTATTGCTAAGGTTAAACAGACGACCCCCTATAACAGATCGACAGCACCTCGTGAAATTGGGCCTCATAGCACGTGTATTAAACACCAGATGGTGAACCATTGTAACAAGCTAACTAGAAAATCTGTCCTGGTTGATTACGAACAAACTTATACTTGGAATTTGTGTTAGGTTGGCTGTATCAACCTTAAGCTTAAGTACAATTTTGCATAGAATGTCCAATAACCCTGAGTTGAACATTACCAGCCTGTACCAAGAAATTATGATTAGACTTACGAATGAGTAAATCTTCATAATTAGGGTTAAGCATGTCTTCAGAGTGCAGATCACATGTCTTGGACAGTAGCTTCCTGATGTCATCAAGCCAAAGACCGTTGGTGTAGTTTGTACCACAAGTTACTTGTACCATACAACCCTCAACTTTACCAGATGGGAAGGTGCAATGATTCGTTTGTAGTCGTCTGTTTAACTTATACTTAATACATATT\n++\n+(%&##%*/;1+\')/3279::;>62<89/@=;12,)%)$/\'&(%%%#&%%\'\'+),79::B3/57531$&&110,++)-15889?735)/0+$(%$&#%&(/8.,-2/:9682:/@4:=DDAGEA=22((/+*%%&#&&&%7989++.2,.9.*%%%$%%%)2./)%%%/))&\'(&)#$$%&&&#.+)\'6+/49/.,52/;896:9:7985585768-BCEAGOJ>@<=>=:@5567?&\'#//5:B8;1?3@?==>====?;HDE<D>2-7:2.+35767(899KB=??;TI<==<A<89>;:<@=?IB7BAFGGFFECC=:/0*\';72-*(\')$$%*)%,443/4-2\'$+78A>?@>+&$(+%$$%%)&)\'\'&*51+<::7D@FG9,;;96<6#\'+,+)8.5=(%%786>>>::0)278<52??..8;321\'#(5269:<405<>9A<27<4;+0+%&&&&%%*.%%$4<94063-,0)@;;<=\'\'&,-(%%$$$))%#$%#$%\'\n' 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| diff -r 000000000000 -r 7a82006f7c05 test-data/SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta Fri Aug 27 20:34:52 2021 +0000 |
| b |
| b'@@ -0,0 +1,500 @@\n+>SRR11410539_seqtk_sample_500_1.fastq/ARTIC/medaka 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|
| b |
| diff -r 000000000000 -r 7a82006f7c05 test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Fri Aug 27 20:34:52 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - dbkey (Database key) +# - name (Galaxy shows this in the UI) +# - path (the reference file) +# +test_entry test "Test Reference" ${__HERE__}/nCoV-2019.reference.fasta |
| b |
| diff -r 000000000000 -r 7a82006f7c05 test-data/gupplyplex_output.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gupplyplex_output.fastq Fri Aug 27 20:34:52 2021 +0000 |
| b |
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| b |
| diff -r 000000000000 -r 7a82006f7c05 test-data/nCoV-2019.V1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nCoV-2019.V1.bed Fri Aug 27 20:34:52 2021 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 7a82006f7c05 test-data/nCoV-2019.reference.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nCoV-2019.reference.fasta Fri Aug 27 20:34:52 2021 +0000 |
| b |
| b'@@ -0,0 +1,500 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CGTAA\n+TCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTG\n+ACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACA\n+AATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACA\n+GGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGACAATATTGCTTTGC\n+TTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAG\n+ATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA\n+AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGAT\n+GAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTG\n+ATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTA\n+CTTTTAAAAGAACCTTGCTCTTCTGGAACATACGAGGGCAATTCACCATTTCATCCTCTA\n+GCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGAC\n+GGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACTGTTCATCAGA\n+CAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT\n+ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACT\n+TCTATTTGTGCTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTT\n+GGTTCTCACTTGAACTGCAAGATCATAATGAAACTTGTCACGCCTAAACGAACATGAAAT\n+TTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTAC\n+AGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATT\n+CTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGG\n+ATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT\n+GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTT\n+CGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAA\n+CGAACAAACTAAAATGTCTGATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTAC\n+GTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACGCAGTGGGGCGCG\n+ATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCT\n+CACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACAC\n+CAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG\n+TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGG\n+GCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGA\n+GGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGC\n+AATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAG\n+CAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAA\n+TTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGA\n+TGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG\n+TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAA\n+GAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAG\n+ACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAAC\n+TGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGG\n+AATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGC\n+CATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCA\n+TATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC\n+TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCC\n+TGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTC\n+AACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGC\n+TTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGC\n+ACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCTTTAATCAGTGTGTAACATTA\n+GGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTACGATCGAGTGT\n+ACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT\n+TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAA\n' |
| b |
| diff -r 000000000000 -r 7a82006f7c05 test-data/nCoV-2019.scheme.V1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nCoV-2019.scheme.V1.bed Fri Aug 27 20:34:52 2021 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 7a82006f7c05 test-data/primer_scheme_bedfiles.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primer_scheme_bedfiles.loc Fri Aug 27 20:34:52 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (the primer scheme bedfile) +# +test_entry "Test Database" ${__HERE__}/nCoV-2019.scheme.V1.bed |
| b |
| diff -r 000000000000 -r 7a82006f7c05 test-data/test.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fastq Fri Aug 27 20:34:52 2021 +0000 |
| b |
| b"@@ -0,0 +1,40 @@\n+@8db09f2a-de97-4ebd-80ac-fdd69d356cad\n+TGGTCCATGTAACTACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTTAAAATCTGTGTGGCTGTCCTCCGGCTGCATGCTTAGTGCCACTCACGCAGTATAATTAATATTAATTACTGTCGTTGACAGGACCTTTTTGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTTTGTCGATCATCAACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAGATGGAGAGCCTTGTCCCTGGA\n++\n+%&%$&$$##$$((%'(:7=@8,>@@C=DB;;>EG;:44456<7CC=<4:)21'-,,06::93;?@?9:=5:3<>?@B?+,0053%(&$$)566)*-)7<9//(&.=0.))*)44;CA@>94--%%21-.77;?=@3*19-((?6$/0/1322(#3572:;??<?ADDFJI?>??@AACFB@LGCADNBQK=?;<@>A@B<.,0%5676830370128=75A<COI;=++A6,-/.D@=DGB>?C;942(+--.-,*423/<=<>=42))&#\n+@9518353b-8dcc-460f-9801-2be35ffc6a19\n+AAGCATGCTTCGTTCAGTTACGTGGTAACACCAACCAACTTTCGATCTCTTGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTCTCTCGGCTGCAATAGTGCACTCACGTGTAATTAATAACTAATTACTGTCGTTTGACAGGACCTGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCCATCTAGGTTTTGTCGGGTGTGACCGAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGGAAAACACGTCCACTCAGTTTGCCTGTTTTACAGGTTCGCGACGATGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGGCACGTCAGCATCTTAAAGATGGTAATACGTAACTTAAGCATGCTTCGTTCAGTTACGTGGTAACACCAACCAACTTTCGATCTCTTGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTCTCTCGGCTGCAATAGTGCACTCACGTGTAATTAATAACTAATTACTGTCGTTTGACAGGACCTGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCCATCTAGGTTTTGTCGGGTGTGACCGAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGGAAAACACGTCCACTCAGTTTGCCTGTTTTACAGGTTCGCGACGATGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGGCACGTCAGCATCTTAAAGATGGTAATACGTAACTTAAGCATGCTTCGTTCAGTTACGTGGTAACACCAACCAACTTTCGATCTCTTGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTCTCTCGGCTGCAATAGTGCACTCACGTGTAATTAATAACTAATTACTGTCGTTTGACAGGACCTGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCCATCTAGGTTTTGTCGGGTGTGACCGAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGGAAAACACGTCCACTCAGTTTGCCTGTTTTACAGGTTCGCGACGATGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGGCACGTCAGCATCTTAAAGATGGTAATACGTAACTTAAGCATGCTTCGTTCAGTTACGTGGTAACACCAACCAACTTTCGATCTCTTGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTCTCTCGGCTGCAATAGTGCACTCACGTGTAATTAATAACTAATTACTGTCGTTTGACAGGACCTGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCCATCTAGGTTTTGTCGGGTGTGACCGAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGGAAAACACGTCCACTCAGTTTGCCTGTTTTACAGGTTCGCGACGATGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGGCACGTCAGCATCTTAAAGATGGTAATACGTAACTT\n++\n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n+@9bd6c9e7-e630-471b-88f5-f0f46e5b3767\n+CATCGGTGTTGGCCCGTTTCAGTTACGTAACCTACCAACCAGCTTTCGATCTCTTGTAGATCTATTCTCTAAACGA"..b'GCATTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCGTCAACATCTTAAAGATGGTAATACGTAACTTG\n++\n+#$$""&+0.<C;BEE<>?<<;9\'%$$##&$$555:2\'\'+99<?@@=8C7EAB;+(4<=AGHGCHD:KGH5694\'\'@FOF93;=66-=0==<=:470+1:>=?9636@A=E586?;<=CFJA@8\'\'*CD?A?<<:68@5:?F526AAHFAC-;<?7..C54922//79695=;;:;@??KB=6(\'\'0311106;>ACEHDCA9=B@@EDA>A<=AB=@664/68:363/8,,26<GH-\'7$37>7339DI@:CA8?9EA>;)$$$4*45237>B@-?79BEFCG<5892%*+)$%\'$%4$%::7;;@/?AE;@CDF@EFH=;;<3><69769444)*((,\'\'+253>63119<=<;8??BJG@C@>4%%-9><=G:=77),$%1\'*7:<5640)++58463..\',-+(.53341##$$\n+@74fdf93b-4411-4aba-8346-7c443da2eead\n+GTTGTACTTCGTTCAGTTACGTGACAACACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTCGTGCAGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAATAATTACTGTCGTTGACAGGACTGAGTAACTCGTCTATCTTCTGCAAGGCATACGGTTTTCGTCCGTGTTGGCAATCCATCATCGGTTTTTTGTCGGGTGTGACCGAAAGGTAGATGGAGAGCCTTGTCCCTACTGGTTTCTTGAAAACACACGTCACTCGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTATTGGCTTTGGAGGCTGTGGAGGATATATCAGAGGCGTCAACATCTTAAAGATGAGCAATACGTAGCCT\n++\n+#,-.00//9CDH?<16)*%%&#&#&#$#%(\'\'-445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|
| b |
| diff -r 000000000000 -r 7a82006f7c05 tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Fri Aug 27 20:34:52 2021 +0000 |
| b |
| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
| b |
| diff -r 000000000000 -r 7a82006f7c05 tool-data/primer_scheme_bedfiles.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/primer_scheme_bedfiles.loc.sample Fri Aug 27 20:34:52 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +# this is a tab separated file describing the location of primer schemes used for amplicon +# sequencing (e.g. using the ARTIC SARS-CoV-2 protocol) +# +# the columns are: +# value description path +# +# for example +# SARS-CoV-2-ARTICv1 SARS-CoV-2 ARTIC v1 primers /data/galaxy/tool_data/artic_primers/SARS-CoV-2-ARTICv1.bed |
| b |
| diff -r 000000000000 -r 7a82006f7c05 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Aug 27 20:34:52 2021 +0000 |
| b |
| @@ -0,0 +1,13 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of primer scheme bedfiles in the required format --> + <table name="primer_scheme_bedfiles" comment_char="#" allow_duplicate_entries="False"> + <columns>value, description, path</columns> + <file path="tool-data/primer_scheme_bedfiles.loc" /> + </table> + <!-- Locations of reference fasta files --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 7a82006f7c05 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Aug 27 20:34:52 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of primer scheme bedfiles --> + <table name="primer_scheme_bedfiles" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/primer_scheme_bedfiles.loc" /> + </table> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> |