| Next changeset 1:57bf9a0d49a5 (2019-01-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90 |
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added:
all_fasta.loc.sample slamdunk.xml test-data/actb.bed test-data/all_fasta.loc test-data/reads.fq test-data/reads_slamdunk_mapped_filtered_tcount.tsv test-data/ref.fa tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 3fd7458bc861 all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Thu Oct 11 20:33:07 2018 -0400 |
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| @@ -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. +# |
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| diff -r 000000000000 -r 3fd7458bc861 slamdunk.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/slamdunk.xml Thu Oct 11 20:33:07 2018 -0400 |
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| b'@@ -0,0 +1,215 @@\n+<tool id="slamdunk" name="Slamdunk" version="0.3.3">\n+ <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description>\n+ <requirements>\n+ <requirement type="package" version="0.3.3">slamdunk</requirement>\n+ </requirements>\n+ <version_command>slamdunk --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $reference_source.reference_source_selector == \'history\':\n+ ln -f -s \'$reference_source.ref_file\' reference.fa &&\n+ #else:\n+ ln -f -s \'$reference_source.ref_file.fields.path\' reference.fa &&\n+ #end if\n+ slamdunk all -r reference.fa -b \'$Reference\' -o ./out\n+ -n $multimapper.multimappers\n+ $multimapper.multimap\n+ #if $multimapper.filterbed.bedtofilter:\n+ -fb $multimapper.filterbed.bedtofilter\n+ #end if\n+ -5 $quantseq.trim5\n+ -a $quantseq.maxpolyA\n+ $advanced.endtoend\n+ -mq $advanced.minMQ\n+ -mi $advanced.minID\n+ -nm=$advanced.maxNM\n+ -mc $advanced.minCov\n+ -mv $advanced.minVar\n+ -mbq $advanced.minBaseQual\n+ -rl $readLength\n+ -c $covThresh\n+ \'$Reads\'\n+ ]]></command>\n+ <inputs>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" type="select" label="Genome" help="Select a built-in FASTA file (if available) or one from the history">\n+ <option value="cached">Use a built-in FASTA</option>\n+ <option value="history">Use a FASTA from history</option>\n+ </param>\n+ <when value="cached">\n+ <param name="ref_file" type="select" label="Use built-in FASTA" help="Select genome from the list">\n+ <options from_data_table="all_fasta">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No reference genomes are available" />\n+ </options>\n+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the FASTA" help="You can upload a FASTA sequence to the history and use it as reference" />\n+ </when>\n+ </conditional>\n+ <param name="Reference" type="data" format="bed" />\n+ <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" />\n+ <section name="multimapper" title="Multimapper recovery"\n+ expanded="false">\n+ <section name="filterbed"\n+ title="Use separate 3\' UTR bed to filter multimappers." expanded="false">\n+ <param name="bedtofilter" type="data" format="bed" optional="true"\n+ label="Bed to filter" />\n+ </section>\n+ <param name="multimappers" type="integer" min="1" value="1"\n+ label="Maximum number of alignments to report per read"\n+ help="The maximum number of alignments is used to track multimapping read alignments. The more are allowed, the more sensitive the multimapper filtering will be, but also the longer the runtime will be. 100 was used in previous publications." />\n+ <param name="multimap" type="boolean" truevalue="--multimap" falsevalue=""\n+ label="Use reference bed file to resolve multimappers."\n+ help="Enable multimapper recovery, requires -n to be set to a value > 1 to have impact." />\n+ </section>\n+ <section name="quantseq" title="Quantseq" expanded="false">\n+ <param name="trim5" type="integer" min="0" value="12"\n+ label="Number of bp to remove from the 5\' end of all reads"\n+ help="'..b'TA[\n+SLAM-seq\n+========\n+\n+SLAM-seq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. When combined with metabolic labeling protocols, SLAM-seq allows to study the intracellular RNA dynamics, from transcription, RNA processing to RNA stability.\n+\n+Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 <https://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4435.html>`_\n+\n+Slamdunk\n+========\n+\n+To analyze a given SLAM-seq dataset with *slamdunk* without recovering multimappers, you only need to provide the following files and keep everything else to the default parameters.\n+\n+=============== ==========================================================================================================================================================\n+Parameter Description\n+=============== ==========================================================================================================================================================\n+**Genome** The reference fasta file (Genome assembly).\n+**Reference** BED-file containing coordinates for 3\' UTRs.\n+**Reads** Sample FASTQ(gz) files.\n+**Read length** Maximum length of reads (usually 50, 100, 150).\n+=============== ==========================================================================================================================================================\n+\n+This will run the entire *slamdunk* analysis with the most relevant output files being:\n+\n+* Tab-separated *tcount* file containing the SLAM-seq statistics per UTR\n+* BAM-file with the final mapped reads for visualization and further processing\n+\n+------------------------------------------------------\n+\n+Multimapper recovery\n+--------------------\n+\n+To utilize multimapper recovery, modify the following parameters. You must either choose a separate 3\' UTR file or activate filtering\n+on the supplied reference file. Will only yield different results than a unique-mapping run by specifying a number > 1 as maximum number of multimapper aligments to consider.\n+\n+=================================================== =========================================================\n+Parameter Description\n+=================================================== =========================================================\n+**Maximum number of alignments to report per read** The maximum number of multimapper alignments to consider.\n+**Use separate 3\' UTR bed to filter multimappers.** 3\' UTR bed file to filter.\n+**Use reference bed file to resolve multimappers.** Use reference as 3\' UTR bed file to filter.\n+=================================================== =========================================================\n+\n+------------------------------------------------------\n+\n+T>C conversions\n+---------------\n+\n+Depending on the use case, more stringent or more lenient measures of T>C conversion and T>C reads are required such as 2 T>C by `Muhar et al., Science, 2018; http://doi.org/10.1126/science.aao2793 <http://science.sciencemag.org/content/early/2018/04/04/science.aao2793>`_\n+\n+This can be controlled by the following parameter:\n+\n+============================ ================================================================================\n+Parameter Description\n+============================ ================================================================================\n+**T>C conversion threshold** Minimum number of T>C conversions to consider a read as T>C read.\n+============================ ================================================================================\n+\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="bibtex">\n+ @misc{Neumann2018,\n+ author = {Neumann, Tobias},\n+ year = {2018},\n+ title = Slamdunk},\n+ publisher = {GitHub},\n+ journal = {GitHub repository},\n+ url = {https://github.com/t-neumann/slamdunk},\n+}\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 3fd7458bc861 test-data/actb.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/actb.bed Thu Oct 11 20:33:07 2018 -0400 |
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| @@ -0,0 +1,1 @@ +chr5 120498 122492 Actb 0 + |
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| diff -r 000000000000 -r 3fd7458bc861 test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Thu Oct 11 20:33:07 2018 -0400 |
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| @@ -0,0 +1,1 @@ +hg38full hg38 Human (Homo sapiens): hg38 Full ${__HERE__}/ref.fa |
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| diff -r 000000000000 -r 3fd7458bc861 test-data/reads.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fq Thu Oct 11 20:33:07 2018 -0400 |
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| @@ -0,0 +1,48 @@ +@Read1_1_0 +CCGTTTGTGTAAGGTAAGGTGTGCACTTTTATTGGTCTCA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@Read2_0_0 +TTTGTGTAAGGTAAGGTGTGCACTTTTATTGGTCTCA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@Read3_1_0 +CTTGTGTAAGGTAAGGTGTGCACTTTTATTGGTCTCA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@Read4_1_1 +TCTGTGTAAGGTAAGGTGTGCACTTTTATTGGTCTCA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@Read5_2_2 +CCGTGTAAGGTAAGGTGTGCACTTTTATTGGTCTCA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@Read6_1_0 +TTGTGTAAGGTAAGGCGTGCACTTTTATTGGTCTCA ++ +FFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFF +@Read7_0_0 +CACACCCACCCAACCTGCTCCCCACACCCAGCAAAGCCACAGAGCCACAAGCTGTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@Read8_1_1 +CACACCCACCCAACCTGCTCCCCACACCCAGCAAAGCCACAGAGCCACAAGCTGTC ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@Read9_1_0 +CACACCCACCCAACCTGCTCCCCACACCCAGCAAAGCCACAGAGCCACAAGCTGCT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@Read10_0_0_rev +TGAGACCAATAAAAGTGCACACCTTACCTTACACAAAC ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@Read11_1_0_rev +TGAGACCAATAAAAGTGCACACCCTACCTTACACAAAC ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@Read12_1_0_rev +TGAGACCAATAGAAGTGCACACCTTACCTTACACAAAC ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF |
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| diff -r 000000000000 -r 3fd7458bc861 test-data/reads_slamdunk_mapped_filtered_tcount.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads_slamdunk_mapped_filtered_tcount.tsv Thu Oct 11 20:33:07 2018 -0400 |
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| @@ -0,0 +1,2 @@ +Chromosome Start End Name Length Strand ConversionRate ReadsCPM Tcontent CoverageOnTs ConversionsOnTs ReadCount TcReadCount multimapCount ConversionRateLower ConversionRateUpper +chr5 120498 122492 Actb 1994 + 0.0222222222222 666666.666667 445 90 2 8 4 0 -1.0 -1.0 |
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| diff -r 000000000000 -r 3fd7458bc861 test-data/ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref.fa Thu Oct 11 20:33:07 2018 -0400 |
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| b'@@ -0,0 +1,2 @@\n+>chr5\n+CACCTGGGCACAGTCAACAATGGATAAGGAGTGTTCTACCAGGAAACAGGCATAGGCCAGCTGGAGCACTGGGTGATGCAAAGAGAGACACCGCTGAGCTGAGCAGGATGGGGGGGAGGGGGAGgggagtgacagcacaggcctttaacttgtgcagagacaggagtgtctctgtgaattcaagcccaacctgctctgtgtagtgagttttttcctcatcagggctccataatgaaacccccatctccagaaaaataaCAATAGCGCAGGCAAATAGACCCAGGCACAGCACTGCACCTCCCGGGGGCAGGGCGTGTCCCAGAAGCCTGCTCTGACATTACAAATGGGTCAGAGTGAGACAGAACACCTGGCCTTGCTAGGTTGTCTGGGAAATAAGCCTTAGAGGATTCCAGGGGAGAGGCCACAGAAGGGGCTGCTAGCAAAGACCACAAAACCCAGAAGGCAGCAGGAGGCAGGCaggggaggggaggggaggagaggggaggAACCCAGGAGATGGCAGGAGATACAGGTATGGGTGTCTAGTCTGGAAATCGCATGGGAGCATCTTTTCCTGGTAGGTGACCCTGGGCTGTGGTCTAAGAGGCTGGGGACATGGAACAATGCCTGCCTGGCTTGAGATGTTGCACAAGCAAGGACCAGCTGGACGTGATCTTTTCTGGGCCGTCACTCAGCCTGCCATGACATCACCAGGGTACACCCGAGCAGTTTCAATGCCTGGACCCACAAGGCCCTCAGCACGGCAGCAGGCTCTGCCCTTAGCTGACACGGTACAGGGCTCAATAAACATGTTGAAGATCAGTCTCCAAAATACACAAGGACTCAAGGACACCGACCAACTTACCAAGCTCTGGGGAAAGATTCAACCTCACTGTGAATTAAAAGAAACAAGCCCAGgccgggtatggtggcgcacacctttaatcccagcactccggaggcagaggcaggcggatttctgagttcgaggccagcctggtctacaaagtgagttccaggacagccagggatatacacagaaaccctgtcttgaagaaaaaaaCAAACAAACAagtccagtgtggtagctaaaacccgcaacggcagcacttagggtaacaaggttgagggtagtttgcctcagccttggctataacaagacctcatctcaaaacaacaaaaAAAAGGGGGACGggggggggagatggctcaacagatacagtgcttgctgtgcatggccaaggacagcagttcagatcccatgtcggagctcttacaatgaaataggaggcaaaggctggggagtcccccaaaagcccacaaacctggcagcctggtggacacagtaagaaactgtgtgaggccctgccgtaaacaaggtagacagcaaggactgacacccagattgtcctctgaccttaaaataggcacatggcacacaAATGCCCAGATACTCACAGGAACtctgtctgtctgtctgtctgtctgtctgtctgtcacacacacacacacacacacacacacacacacacacacgatagacagacacacaAagacatgacaggtagacaaatagccagacaggcagacagacagacagacagGAAAATGAAAGGGACAAAAAAAAGTAAGCTGAgcgaaataatccggtggccacaactgcttgccacacaagcttgccgacctgaatttggccccctgagccctgcaggaggagaatcaactttaggaagtttttctctgtcctccctatctgcacacagcaagcacacgttcagacactcatgcccaTGCGCACACCCGCTTGCGTGTGCGCACACACAACTGATAATAAACAATCATTTTACAAAAGCAGCAGCAGCAAGTTGGGTGccattgatggctcagcaggtgaaagggatgtgaggcccatttctcagctctgtgggcactaacacacatgtgacacacatatgacacacatgcaCATACAgttttggttttgttttcttgtggttttggtttttgttttgttttgttttgttttCCAGTTAAAAAAGATTCACTAAAGCCTGTCAGGAAGCCGCCTCTTACTATTCAAAAGcattcattcattctttcattcattcattcattcattcattcaCCTGGTTCCCCAGCACCCTCCATGCTCCAGGCCCCGCGCTGACTGGACCCCAAGAGGCACTGAATGAGTCAACACCGGGCTCTACCCCACTGGAAGGCTTACGGTTGGTCTATTCCTAGGAATCCCTAGGACAGAACAAAGCGACTCAACACAGCACAGAGGTGCTTACGTGCAAAAATATTCCACACAGCGTTCTCCACACAAAAGAGAGCAGGCAAAGACTGAAAATGCCCACCGGGGAATGGAGACCTAACTACAGTACCTGCTGCTGTGTGCTCTCCACAGAATATTAAAGGCCGTAAAAAAAATGATACTTGTAAAGATTCTGACATCTCGGGAGAAACAACCCACACTGTGCTGCGGGAGCGAGCGTAAGACCAAGGCTGTGCCACGCTAGCCGCTCCACAGGTAGACACAAATTGCATGGGAAAATGAATTCAGGGAGAGCCGGGAAAGTGTTTGGGGTGCTGGGGAAACAATAATGGTCTTTTTCTTCGTTCTCCTCTCCTGCACTCTACACATCTATGTGGATAATGGGAAAGGCAATCAAAGTTTCAATAGCAGCCACGATGGGCAAGTGGGGAACAGGCATGCAGTACTAggagggagggagaaagggagggagtgagggaggatgggaggATTGGGAGAAAAGACCAAGAAACCAgccaggaatcccagcactccagaggtagagatgaggggatttctctgagttcaaagccagcctggtctacatagtaggttttgagctagccaggactatactgtgaaagcccatctttaaaaaaacaaaaCAGTgctggagagatggctcagtgggtaagagcactgactgctcttgcagaggtcctgagttcaattcccagcaatcacatggtgactcacaaccatctgtaatgggatctgatgcccacttctggtgtgtctgaagacagctacagtgtacttacatacataaaataaataaataaataaaaacaaaaTAGGAAGCCAGAGGCAGGGAGAGACAAGAATAGGGATTGGgccaggcagtgtgacacacactgttaattccagcactcaggaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcagaggcaggcagacctctgtgacttgaggctagcctggtctacagagtgagttccagggcagccagggctacatgaagagccctatctcataaaaccaaaaAGAACAAAAAGCAAAAAAAAAACAAAACAAAAAGGGCCAGATATGAGGCAAAGAATCTGTGTCTGCAGCCCCAGCGAGAGAGACTGTCCCCAGACAGTCaagtaactccgtgtgtaaaggcacctgaagacctgggttccatccccaaaaccccaaaacccacgtgctagaggaggagccatttcttataagttatcctctggcttccccatgtgcactgtggtgcATTCTCATGGCTGTGTGGGATacacacacacacacacacacacacacacacacaGAGAGAGCAAACACAGTaagacagaacaaacacccaaggttgtcctctgacctctacacttgcacgtaacacctgtccccacacccacacccaAACATTAACATTTAAGGAGAGTGGGGACTATTCCTGCTTTAATTCCCAACttttttttttttttagatttatttattacatgtaagtacactgta'..b'ctcagtttcctcactttcaaattgagggcataatattctcatgtagttttggaattcagataagatataaggccatctgacatgatgtgtggcaTTTTTTCATTCTAGGACTCCTGCAGGCTGTCAAGAGGGAGAAGAAACTCGGCTCCTTCCTAAACCAAACCTGGTCTGTGCAAAGCTAGTGATTTAAGAAGTGGGAGCCAAGTCTATATACACTGGATCTCTGAATACTTGGTCTGGGAGTAGGCAATCCCTCTGTTGAAGGAGCACACGTCCAAGCTCACACTCCTACAGTCCCCCAATAGCGAGACTGTTTCTAGAAGCATTTCAACTGATAAGGAGGGCCCACTACTGCCAGGATACTTCTTACTGTGTTGGTATTTTGTATTGCTGCTCCCAACTACAAACCGACACCCTTCACCTTTCTCTGTTACACTGAGGGCCTTGAAGACAGAGGGAAGGGAGGCAGGATCAAAACAAATTTGCTATTGAGATAAAGGGTGGGTGGCCAGCTACAAAGTGAAGCAGAGAGGGTGTCCAGCAGGATGTGCTGCGATGTAAAGGTGAGTGCAATCTAGGCAGCAAATGCTTTCACTGTGTGCACTGCAGCTACTCACACTGCAGCAGTTTGTCACTTAGACACCAAACTATGTACCAAGAACAGTAAAATGCAATATAACACTGGCTGCTACTTATTGAGGTCCAATCTGCTAGTGACCTGAAATGAAGAAAAGCAGAACTTTAGCTTGGAAACAATCTACACCCAGTTCAAGTTACAGAAGAACAAATGATTTCTAAGTTTTGTTTAATAGGAGACCAAGTTTAACTAAttaatcttttgaatcagggtgtcacaaagcctaggctggcctggagctcaccacttgactaggctgaccttgaaatcagagagatccatctgtgtctgcctcctgaactgggacccagtgtgtccaggagactagactctattacTACTGCCGGCTGGGAGTAGCACAATGAGTTTAGTTACTGAGCAACTGTGAAGACACTTCTTTTTTTTTttttggttttttgagacagggtttcccgtatagctctatagctctggctgtcctggaactcactctgtagaccaggctgtcctcgaactcagaaatccgcctgcctctgcctcctgagtgctgggattaaaggcatgtaccaccacgcccggctCATGAAGACACTTCTTAATGTTGCTTCTTAAGATGCAAGGAGCTgctgggtggtggcggcacacacccttaaccccagcacttgggagttcaaggccagcctggtctacagattgaattgtaggatagccaggaccatacaaagaaaccctgtcctgaaaaaCCTCCACCACCACCACCACCACAACAAAAACAAAACAGAAAAGGCCAGAATGGGCCTATATAAGAAAGGACTGCGGCTGTATGGAACAGAGAAGCCACAGCTGCTTTTTGTTGTTAGCGTGAACTATACAGGAAAGAGCCTCACAGGATGTGCTTCCAGAAGCAGGACAGGAAGAGAAGCCTAAGCCGAGGCTGTCTCTGTCTGCTGATCTCATGTTCAACAGGAAGACTCATGGACATCCTCTGTGCAGCCAGCTGACACCCCACCAGTCTGTCACTACTCGTGCTTTACTCCCCAAAGACAACGGGAAGTAATCTTGGGGGCTTCCTTCTCTCTCCACTCTCCACACCTTCTCTTCCCAACCAAAAACATactctgcagtactggctggtctggaactccctatgtagacaagcctgatttcaaatttatagagaccacctctttctcttgagtgctggcattaTAAAGAATTCTTAAAAAAGAAaaacaaacacacaaacaaacaaacaaacaaaATTTAAGAACTACGGTAgggttggaggagatcgtttagttggtaaagtgcttgacacatacaagcatgagaacttgaactgagattcccagcacccataaaaaagccaagtgtagctgtgcatgtctgttagtccagtactggagaggtaaagacaggaccatccctggggtctgctggtcaacaagtcctgctgaattagctgagttctaggctcaatgagaaaccatgcctcaaaaaaaaaAAAAAAAAAAaaaaggcttagaatgtgggacgattgtgaccaaccctgaggacctgtgtccctgggacccagatggtagaggcagagaagtgattactcatagttgctctttgatttttcataagcCATGTGTCTGTATACATTTTTTTTTTCATTTAAGagacagggtctcatcaggcctttaatctcagtacttgaagcagagacaggcgaatttctgcgctctaggccagcctggtctaccgagcaagttccagtagagccagagctatacagagaaaccctgtctcaaaaaaccagggacagggtctcattgtatagttttggctggccttgaattttgtatgtaagctgggctgatttccaaatcacagaaatccatttgcccctgcctcctaaagctggtataaagatgtatctaccatgcccAACACATAATTAAAAAAAAAATGCCTTAtttaatcttaagtatatgagtgttctgcttgtatatgtgtgtgcaccatgtgcatgcctggtgcccatggagtttagtctgatctccacagactcaagtaatgggaggtaaagagtgacccagcacgcagctgctagggaagaatactcggtcattttatgtcaacgagacacaaactagacttagctgagaggaagggacctgaactgagaaattgtctgtataagagccagctgtagggcatttcttaattatccatctatgcaggagcacccagctcattgtgggtgctgccattcctaggctggtggtcttgagttcagtaagaaagcaagccatgaggaacaaaccagtaagcaacgcccctccatggccgtcacagcagatgctgcctccaggtgcttttcctgactccctttgatgatggatctggaagtgtaaaccaaataaaccctttcctgcccaagtcacgttggtcctggggattcatcccagcaatggGACAAAGAGCAGTGTGCTCTTAAATGCTGAGGCACTGATCTCATCCAAATAAAGATATTTTTCAATTATAAAAAGATGGAGAGAGACAAATGAAGAGGCATCTACACACATACAACACATAACTCACCCATCCCCCCCCCCCCCCCAATCATTCTGGTGTAGTCACCCTAACAGTCACTTTGCCACCACTCCTGACTCATTTTCTTAAAGAAGTATGTACTGAAATGATCTTGCTGGTTTCATGATCTCTGTCTATTTgggctgagaccagctctgtgggagaacatttgtcaagcatgtgtaaggccctaggttaaatttctagAATTGAGAATCCGCTAACAAAGGAATACCTGCCGCCACAAACCCAAAGCACttctctactttttcttggcttttagcagtttgactctcatgtgtcttgtttcagacttaaaaagtactggttcatgtccctaaatctgaaaagttttcagccattctttattcaaatattctctggccccttttataccctctgaataggaatataccagataatgggtcataggtcccttagggttcatacattgcttttctttattcttttcttcccatcttcccaactggataatgtcaGGTAAGTCTGATTCATCACTTTTCTCAAtttattcattctatgtgtactaagtgttttgtcttcatgtatattaagtgtaccacttgtgcacacagtgccctcaaaggccagaaggcagcactggatcctctcctccccagaacctgagttggagacagctgtgagctgccacatgggtttgattcaaacctgggtcatctgaaagaacagccagtgtttgttacccatgagtcatctcGAGCTTCTTTCTTttttgtttttttgagacaatgtctaatgtagacatcaaatgtgctattta\n' 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| diff -r 000000000000 -r 3fd7458bc861 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Oct 11 20:33:07 2018 -0400 |
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| @@ -0,0 +1,8 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> + |
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| diff -r 000000000000 -r 3fd7458bc861 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Oct 11 20:33:07 2018 -0400 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> |