| Next changeset 1:20165d3a8fb1 (2020-06-10) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6" |
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added:
artic_minion.xml test-data/SRR11410539_seqtk_sample_250_1.fastq test-data/SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta test-data/all_fasta.loc test-data/nCoV-2019.V1.bed test-data/nCoV-2019.reference.fasta test-data/nCoV-2019.scheme.V3.bed test-data/primer_scheme_bedfiles.loc 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 c411e2205442 artic_minion.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/artic_minion.xml Thu Apr 30 04:05:09 2020 -0400 |
| [ |
| @@ -0,0 +1,110 @@ +<tool id="artic_minion" name="ARTIC minion" version="1.1.0_rc2+galaxy0"> + <description></description> + <requirements> + <requirement type="package" version="1.1.0_rc2">artic</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + mkdir -p 'scheme/name/version' && + #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table": + ln -s '${primer_scheme_source.primer_scheme_bedfile.fields.path}' 'scheme/name/version/name.scheme.bed' && + #else: + ln -s '${primer_scheme_source.primer_scheme_bedfile}' 'scheme/name/version/name.scheme.bed' && + #end if + #if str( $reference_source.reference_source_selector ) == "history": + ln -s '${reference_source.reference}' 'scheme/name/version/name.reference.fasta' && + samtools faidx 'scheme/name/version/name.reference.fasta' && + #else: + ln -s '${reference_source.reference.fields.path}' 'scheme/name/version/name.reference.fasta' && + samtools faidx 'scheme/name/version/name.reference.fasta' && + #end if + artic minion + --threads \${GALAXY_SLOTS:-1} + --normalise '${normalise}' + --read-file '${read_file}' + --scheme-directory 'scheme' + --medaka + $bwa + 'name/version' + '${read_file.element_identifier}' + ]]></command> + <inputs> + <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/> + <param argument="--normalise" type="integer" min="1" value="200" max="2000" label="Coverage normalisation depth"/> + <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/> + <conditional name="primer_scheme_source"> + <param name="primer_scheme_source_selector" type="select" label="Select a primer scheme from your history or use one from a tool data table?" + help="Screening files must be stored in the 'primer_scheme_bedfiles' tool data table"> + <option value="tool_data_table">From tool data table</option> + <option value="history">From history</option> + </param> + <when value="tool_data_table"> + <param name="primer_scheme_bedfile" type="select" format="bed" label="Primer Scheme"> + <options from_data_table="primer_scheme_bedfiles"> + <validator type="no_options" message="No primer scheme .bed files are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="primer_scheme_bedfile" type="data" format="bed" label="Primer Scheme" /> + </when> + </conditional> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in reference?" > + <option value="cached">Use a built-in reference</option> + <option value="history">Use a reference from history</option> + </param> + <when value="cached"> + <param name="reference" type="select" label="Using reference genome" help="Select genome from the list"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No references are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="reference" type="data" format="fasta" label="Use the following dataset as the reference sequence" + help="You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="alignment_trimmed" format="bam" from_work_dir="*.trimmed.bam" label="${tool.name} on ${on_string}: trimmed alignment" /> + <data name="variants_tabular" format="tabular" from_work_dir="*.variants.tab" label="${tool.name} on ${on_string}: variants table" /> + <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: variants vcf" /> + <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="${tool.name} on ${on_string}: consensus sequence" /> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history" /> + <param name="read_file" value="SRR11410539_seqtk_sample_250_1.fastq" /> + <param name="reference" value="nCoV-2019.reference.fasta" /> + <param name="primer_scheme_source_selector" value="tool_data_table" /> + <param name="primer_scheme_bedfile" value="test_entry" /> + <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" /> + </test> + <test> + <param name="reference_source_selector" value="history" /> + <param name="read_file" value="SRR11410539_seqtk_sample_250_1.fastq" /> + <param name="reference" value="nCoV-2019.reference.fasta" /> + <param name="primer_scheme_source_selector" value="history" /> + <param name="primer_scheme_bedfile" value="nCoV-2019.V1.bed" /> + <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" /> + </test> + <test> + <param name="reference_source_selector" value="tool_data_table" /> + <param name="read_file" value="SRR11410539_seqtk_sample_250_1.fastq" /> + <param name="reference" value="test_entry" /> + <param name="primer_scheme_source_selector" value="tool_data_table" /> + <param name="primer_scheme_bedfile" value="test_entry" /> + <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" /> + </test> + </tests> + <help><![CDATA[ +This tool aligns MinION reads that were generated from a tiling amplicon library against a viral reference sequence. +It generates a consensus fasta file and a vcf variant file. + +This tool is configured to use the experimental 'medaka' variant caller. + ]]></help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r c411e2205442 test-data/SRR11410539_seqtk_sample_250_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SRR11410539_seqtk_sample_250_1.fastq Thu Apr 30 04:05:09 2020 -0400 |
| b |
| b'@@ -0,0 +1,1000 @@\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"ACAGAGTACAGTGAATGACATGAGAATAGTAAAGTATTAAAGGCAACTACATGACTGTATTCACCAAAAGCTCTTCTAAACCTCATAAAATAGTAGGCAAGGCATGTTACTACGATGGCTACAATACTGCCAGCTACTATAGATGCTGATATGTCCAAAGCACCAATAGGTTGAATTAGTGGTGTAAACATATTAGTAAGTAAATTTACAGCATCTACACCACAGAAAAACTCCTGGTAAAGATCTGTAATAATCATTGTTAAGTACCCATCTACCACTAGTAGATACACAAACACCAACTTCTGATCTTCACAAGTGCCGTGCCTACAGTACTCAGAAAGGTGCTGTCGATTCCGTTTGTAGTCGTCTGTTT\n++\n+&$*%-%36;:<K<@8:FCA.>A??A3/@;;3CDFHJG=A<A9?<83(278%3%('%%5;:>+A&<?FFI>CEA@G><:53)(4**/?CC2BH+78@>GJ;9<;A>HDCCD=1''&$+,688ADCC:>648/*+58@BH@=67//+4&&&*2+<B@1)3B>;698<@BA<<<A=<>OQ?,5B:;:8:6@CCA>F??BFMFM<G?9=8<<=?DEFIADHEC><=7./1$-;<>>C5,+$%%67@CEEIBEEB=>8CA@6253A<;339*+).;;77CD?F9BBBA>=6879B<<ABA?HD>:FFKB12>8:=CHI@HG3*+133B>DFD@F>2;<?7977?6?D79B47G<<52?:<C>:<GEGI?BAGG;=@78>=:HEAB<<?82>??5.7-6-8?AA=BDE<88CA96)).(+9:;=?4324=?>K>BA':A@>;>>;CF61364.0.,AEG=>>:76==DB787C:F9@B<9969;A=74+\n+@SRR11410539.2047746 2047746/1\n+CGATGTACTTCGTTCAGTTACGTATTGCTAAGGTTAAACAGACGACTACAAACGGAATCGACGGCACCCGACGAATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGAGTAGGTTTGTACTTGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCTAAGAGTGATGGAACTGGTACTATCTATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAGGTCCTAAAGTGAAGTATTTATACTTGCATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCGCTGGTACGTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAGGTGCTGTCGATTCCGTTTGTAGTCGTCTGTTTAACTATAACCAATACAT\n++\n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n+@SRR11410539.2123302 2123302/1\n+CACGTACTTCGTTCAGTTACGTATTGCTAAGGTTAAACAGACGACTACAAACGGAATCGACAGCACCTCATGGCTGCATCACGGTCAAATTCAGATTTAGCCACATTCAAAGACTATTCCAACTTTTTAGAACAACTTCAGAATCACCATTAGCAACAGCCTGCTCATAAGCTTCTTGAGCAGTAGCAAAAGCTGCATATGATGGAAGGGCTAAACTCTGAGGCTATAGCTTGTAAGGTTGCCCTGTTGTCCAGCATTTCTTCACAAAGCTTGTTTATGTCTACAGCACCCTGCATGGAAAGCAAAACAGAGAAAGTAATTTGAACCATTTTCAAAGGCTTCAGTAGTATCCTTTAGCTAAGAGAATGTCATTGTGTAACTGGACACATTGAGCCCTGAGTTAGATGATGATTCTACTCTGAGTTGTTGCAAACGAGAACAGAACTACTGATGTGCAGGTGTCGATTCCGTTTGTAGTCGTCTGTTTAACAACAATAATAT\n++\n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n+@SRR11410539.321039 321039/1\n+CATTGTACTTCGTTCCGGTTACGTATTGCTAAGGTTAAACGAACTGACTACAAAACAGAATCGACGCTTTGGTGTTGTTGGAAAGTTCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAGTGTATCAATATTGTTGGTGACTTTAAACTTAAATGAAGAATCCTTATTATTTGGCATCTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTTGGATTATAAAGCATTCAAACCAAATTATTGAATCACAATAGTAGGTGCAAAGTTACAAAAGGAAAAGCTAAAAAAGTTCTGCCTGGAATATTGGTGAACCAGAAATCAATACTGAGTCCTCTTTATGCATTGCATCAGAGGCTGCTCGTGTTGTACAGTCAATTTTCTCCTGCCTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACCGAAGGCGCGCTAGGTCTTGTCGATTCCGTTTGTAGTCGTCTGTTTAACATAGCAATACGTAA\n++\n+(#%'-.*,,-*;B?(-'-88/*+3398,(6./0>><98+(($%$%,,5:/63477&$(48837//%$%%'/1><EI;DC56(+%&,)-&&%&-(-+266&*0655=>:C@;9++BC=81:)=A?+)%('&%%$.#$2,>>AGGJG2;3.1:;8<AF@:>:?@=:71---1''-%%,%%)(**/5;::;B>@EA=;.**9:8<B?BC:?;9@@?3%335<=0<A==:952&2*.91.3..3;7/03,19<19/1.&+(($%($#%55/('%$%%)&+)%&,1$-??-.5;;89:0(&D@H=:;;=73,&%$*%(&*178>ADD<5566'+/--.%-*&*--1>@6/*+61,711.@AFB8=@DG?CAA?5-4,.&$)/0.5346>><=742,%$&)')%11,.2'-'+0+9>@:=;FA@DCBKDBB@F:>>6/''$%'%###$&%(%%&$'($'$$($('%$%)&-,87=@68:;:3,/..5527:3=?F=728,69<<AA>@:42+)\n" |
| b |
| diff -r 000000000000 -r c411e2205442 test-data/SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta Thu Apr 30 04:05:09 2020 -0400 |
| b |
| b'@@ -0,0 +1,500 @@\n+>SRR11410539_seqtk_sample_250_1.fastq/ARTIC/medaka 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|
| b |
| diff -r 000000000000 -r c411e2205442 test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Thu Apr 30 04:05:09 2020 -0400 |
| 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 c411e2205442 test-data/nCoV-2019.V1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nCoV-2019.V1.bed Thu Apr 30 04:05:09 2020 -0400 |
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|
| b |
| diff -r 000000000000 -r c411e2205442 test-data/nCoV-2019.reference.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nCoV-2019.reference.fasta Thu Apr 30 04:05:09 2020 -0400 |
| b |
| b'@@ -0,0 +1,500 @@\n+>MN908947.3\n+ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCT\n+GTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACT\n+CACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATC\n+TTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT\n+CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAAC\n+ACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGG\n+AGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG\n+CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAA\n+ACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACT\n+CGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGG\n+CGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGG\n+TGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGA\n+TCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGA\n+ACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG\n+CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTC\n+ATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCG\n+TGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCA\n+GACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAA\n+TTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAA\n+GCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATG\n+CAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA\n+GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGA\n+AGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGC\n+ATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGG\n+CTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTC\n+TTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGG\n+TTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGA\n+AATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA\n+GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAA\n+AGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTAC\n+AAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCC\n+TCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCT\n+TGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGG\n+AATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTAC\n+TAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG\n+GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGA\n+AGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTAT\n+CTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAA\n+GGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTC\n+TATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCA\n+CTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCC\n+TCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT\n+AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGA\n+AGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGA\n+AATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATAC\n+CTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGA\n+AGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGT\n+ACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGC\n+CTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC\n+ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGG\n+TGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGA\n+AGAAGGTGATTGTGAAGAAGAAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGA\n+AGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCCACTTCTGCTGCTCTTCAACCTGA\n+AGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGA\n+CGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATT\n+AGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT\n+AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGT\n+AAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGC\n+AGGAGCCTTAAATAAGGCTACTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGC\n+TACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTTTAAGCGGACACAATCTTGCTAA\n+ACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGTGAAGACATTCAACTTCTTAA\n+GAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTATTATCAGCTGG\n+TATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA\n+TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGA\n'..b'ACTCA\n+ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATT\n+GTTGATGAGCCTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTT\n+AATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAA\n+GCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTA\n+ATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCC\n+ATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTA\n+AAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT\n+CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAG\n+CCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAAT\n+GGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATG\n+CCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAG\n+TAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAA\n+TTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT\n+TCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC\n+TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAA\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 c411e2205442 test-data/nCoV-2019.scheme.V3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nCoV-2019.scheme.V3.bed Thu Apr 30 04:05:09 2020 -0400 |
| b |
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| b |
| diff -r 000000000000 -r c411e2205442 test-data/primer_scheme_bedfiles.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primer_scheme_bedfiles.loc Thu Apr 30 04:05:09 2020 -0400 |
| 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.V3.bed |
| b |
| diff -r 000000000000 -r c411e2205442 tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Thu Apr 30 04:05:09 2020 -0400 |
| 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 c411e2205442 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 Thu Apr 30 04:05:09 2020 -0400 |
| 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 c411e2205442 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Apr 30 04:05:09 2020 -0400 |
| 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 c411e2205442 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Apr 30 04:05:09 2020 -0400 |
| 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> |