Added <edam_operation> tag to 'mentalist call' galaxy tool #21
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dfornika
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Mar 24, 2018
* new script to filter Mentalist flag symbols from the calls * Add .travis.yml file (#18) * Added travis.yml file * Added 'Build Status' badge * Update .travis.yml * Update requirements for TravisCI testing * kmer_class_for_locus function no longer exists * Don't test on OS X * Added coverage badge. * Updated macOS install instructions * Updated macOS install instructions * Update README.md * Update runtests.jl * TravisCI testing on v0.5 is broken. * Added <edam_operation> tag to 'mentalist call' galaxy tool (#21) * fixed a bug in the cgmlst download, fasta file decompression could be incorrect in some cases * adding import JSON; was not needed before because some other library was probably loading it, but for the tests we need this explicitly * new messages while loading a kmer db, better idea of how much each large step takes * lots of new unit tests and a new fastq testing file. Coverage should be much higher now. * Change version info for galaxy tools in master branch to 'master' * support for analysing multiple samples * reorganizing the argparse code and a bit of refactoring * adding all multi-sample functionality; better output for novel alleles; parallel downloading for enterobase * small adjustment on a test * Fix c_jejuni_fastq_file filename in test * Adjusted kmer & vote numbers to match smaller test file. * Update conda recipe * Don't convert fasta_files paths to absolute paths (#23) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database
dfornika
added a commit
that referenced
this pull request
Mar 24, 2018
* new script to filter Mentalist flag symbols from the calls * Add .travis.yml file (#18) * Added travis.yml file * Added 'Build Status' badge * Update .travis.yml * Update requirements for TravisCI testing * kmer_class_for_locus function no longer exists * Don't test on OS X * Added coverage badge. * Updated macOS install instructions * Updated macOS install instructions * Update README.md * Update runtests.jl * TravisCI testing on v0.5 is broken. * Added <edam_operation> tag to 'mentalist call' galaxy tool (#21) * fixed a bug in the cgmlst download, fasta file decompression could be incorrect in some cases * adding import JSON; was not needed before because some other library was probably loading it, but for the tests we need this explicitly * new messages while loading a kmer db, better idea of how much each large step takes * lots of new unit tests and a new fastq testing file. Coverage should be much higher now. * Change version info for galaxy tools in master branch to 'master' * support for analysing multiple samples * reorganizing the argparse code and a bit of refactoring * adding all multi-sample functionality; better output for novel alleles; parallel downloading for enterobase * small adjustment on a test * Fix c_jejuni_fastq_file filename in test * Adjusted kmer & vote numbers to match smaller test file. * Update conda recipe * Don't convert fasta_files paths to absolute paths (#23) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Relative paths in db (#25) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Fixed issue with scheme fasta loading during calling
dfornika
added a commit
that referenced
this pull request
Mar 24, 2018
* new script to filter Mentalist flag symbols from the calls * Add .travis.yml file (#18) * Added travis.yml file * Added 'Build Status' badge * Update .travis.yml * Update requirements for TravisCI testing * kmer_class_for_locus function no longer exists * Don't test on OS X * Added coverage badge. * Updated macOS install instructions * Updated macOS install instructions * Update README.md * Update runtests.jl * TravisCI testing on v0.5 is broken. * Added <edam_operation> tag to 'mentalist call' galaxy tool (#21) * fixed a bug in the cgmlst download, fasta file decompression could be incorrect in some cases * adding import JSON; was not needed before because some other library was probably loading it, but for the tests we need this explicitly * new messages while loading a kmer db, better idea of how much each large step takes * lots of new unit tests and a new fastq testing file. Coverage should be much higher now. * Change version info for galaxy tools in master branch to 'master' * support for analysing multiple samples * reorganizing the argparse code and a bit of refactoring * adding all multi-sample functionality; better output for novel alleles; parallel downloading for enterobase * small adjustment on a test * Fix c_jejuni_fastq_file filename in test * Adjusted kmer & vote numbers to match smaller test file. * Update conda recipe * Don't convert fasta_files paths to absolute paths (#23) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Relative paths in db (#25) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Fixed issue with scheme fasta loading during calling
dfornika
added a commit
that referenced
this pull request
Mar 24, 2018
* Merge master into mentalist_v0.2 (#26) * new script to filter Mentalist flag symbols from the calls * Add .travis.yml file (#18) * Added travis.yml file * Added 'Build Status' badge * Update .travis.yml * Update requirements for TravisCI testing * kmer_class_for_locus function no longer exists * Don't test on OS X * Added coverage badge. * Updated macOS install instructions * Updated macOS install instructions * Update README.md * Update runtests.jl * TravisCI testing on v0.5 is broken. * Added <edam_operation> tag to 'mentalist call' galaxy tool (#21) * fixed a bug in the cgmlst download, fasta file decompression could be incorrect in some cases * adding import JSON; was not needed before because some other library was probably loading it, but for the tests we need this explicitly * new messages while loading a kmer db, better idea of how much each large step takes * lots of new unit tests and a new fastq testing file. Coverage should be much higher now. * Change version info for galaxy tools in master branch to 'master' * support for analysing multiple samples * reorganizing the argparse code and a bit of refactoring * adding all multi-sample functionality; better output for novel alleles; parallel downloading for enterobase * small adjustment on a test * Fix c_jejuni_fastq_file filename in test * Adjusted kmer & vote numbers to match smaller test file. * Update conda recipe * Don't convert fasta_files paths to absolute paths (#23) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Relative paths in db (#25) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Fixed issue with scheme fasta loading during calling * Merge master into mentalist_v0.2 (#28) * new script to filter Mentalist flag symbols from the calls * Add .travis.yml file (#18) * Added travis.yml file * Added 'Build Status' badge * Update .travis.yml * Update requirements for TravisCI testing * kmer_class_for_locus function no longer exists * Don't test on OS X * Added coverage badge. * Updated macOS install instructions * Updated macOS install instructions * Update README.md * Update runtests.jl * TravisCI testing on v0.5 is broken. * Added <edam_operation> tag to 'mentalist call' galaxy tool (#21) * fixed a bug in the cgmlst download, fasta file decompression could be incorrect in some cases * adding import JSON; was not needed before because some other library was probably loading it, but for the tests we need this explicitly * new messages while loading a kmer db, better idea of how much each large step takes * lots of new unit tests and a new fastq testing file. Coverage should be much higher now. * Change version info for galaxy tools in master branch to 'master' * support for analysing multiple samples * reorganizing the argparse code and a bit of refactoring * adding all multi-sample functionality; better output for novel alleles; parallel downloading for enterobase * small adjustment on a test * Fix c_jejuni_fastq_file filename in test * Adjusted kmer & vote numbers to match smaller test file. * Update conda recipe * Don't convert fasta_files paths to absolute paths (#23) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Relative paths in db (#25) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Fixed issue with scheme fasta loading during calling
dfornika
added a commit
that referenced
this pull request
Mar 27, 2018
* Merge master into mentalist_v0.2 (#26) * new script to filter Mentalist flag symbols from the calls * Add .travis.yml file (#18) * Added travis.yml file * Added 'Build Status' badge * Update .travis.yml * Update requirements for TravisCI testing * kmer_class_for_locus function no longer exists * Don't test on OS X * Added coverage badge. * Updated macOS install instructions * Updated macOS install instructions * Update README.md * Update runtests.jl * TravisCI testing on v0.5 is broken. * Added <edam_operation> tag to 'mentalist call' galaxy tool (#21) * fixed a bug in the cgmlst download, fasta file decompression could be incorrect in some cases * adding import JSON; was not needed before because some other library was probably loading it, but for the tests we need this explicitly * new messages while loading a kmer db, better idea of how much each large step takes * lots of new unit tests and a new fastq testing file. Coverage should be much higher now. * Change version info for galaxy tools in master branch to 'master' * support for analysing multiple samples * reorganizing the argparse code and a bit of refactoring * adding all multi-sample functionality; better output for novel alleles; parallel downloading for enterobase * small adjustment on a test * Fix c_jejuni_fastq_file filename in test * Adjusted kmer & vote numbers to match smaller test file. * Update conda recipe * Don't convert fasta_files paths to absolute paths (#23) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Relative paths in db (#25) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Fixed issue with scheme fasta loading during calling * Merge master into mentalist_v0.2 (#28) * new script to filter Mentalist flag symbols from the calls * Add .travis.yml file (#18) * Added travis.yml file * Added 'Build Status' badge * Update .travis.yml * Update requirements for TravisCI testing * kmer_class_for_locus function no longer exists * Don't test on OS X * Added coverage badge. * Updated macOS install instructions * Updated macOS install instructions * Update README.md * Update runtests.jl * TravisCI testing on v0.5 is broken. * Added <edam_operation> tag to 'mentalist call' galaxy tool (#21) * fixed a bug in the cgmlst download, fasta file decompression could be incorrect in some cases * adding import JSON; was not needed before because some other library was probably loading it, but for the tests we need this explicitly * new messages while loading a kmer db, better idea of how much each large step takes * lots of new unit tests and a new fastq testing file. Coverage should be much higher now. * Change version info for galaxy tools in master branch to 'master' * support for analysing multiple samples * reorganizing the argparse code and a bit of refactoring * adding all multi-sample functionality; better output for novel alleles; parallel downloading for enterobase * small adjustment on a test * Fix c_jejuni_fastq_file filename in test * Adjusted kmer & vote numbers to match smaller test file. * Update conda recipe * Don't convert fasta_files paths to absolute paths (#23) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Relative paths in db (#25) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Fixed issue with scheme fasta loading during calling * Updated galaxy tool * Removed newline * -s flag not supported * Updated git url in .shed.yml * Fork an unzip process to decompress downloaded cgMLST alleles * Rewrite download_cgmlst_scheme() to handle new zip scheme files from cgmlst.org * Tidy up comments and fix total locus count * Fix test data filenames for L. pneumophila * Add unzip as a conda dependency * variable n_locus not used * Update .shed.yml * Update .shed.yml
dfornika
added a commit
that referenced
this pull request
Jul 26, 2018
* Merge master into mentalist_v0.2 (#26) * new script to filter Mentalist flag symbols from the calls * Add .travis.yml file (#18) * Added travis.yml file * Added 'Build Status' badge * Update .travis.yml * Update requirements for TravisCI testing * kmer_class_for_locus function no longer exists * Don't test on OS X * Added coverage badge. * Updated macOS install instructions * Updated macOS install instructions * Update README.md * Update runtests.jl * TravisCI testing on v0.5 is broken. * Added <edam_operation> tag to 'mentalist call' galaxy tool (#21) * fixed a bug in the cgmlst download, fasta file decompression could be incorrect in some cases * adding import JSON; was not needed before because some other library was probably loading it, but for the tests we need this explicitly * new messages while loading a kmer db, better idea of how much each large step takes * lots of new unit tests and a new fastq testing file. Coverage should be much higher now. * Change version info for galaxy tools in master branch to 'master' * support for analysing multiple samples * reorganizing the argparse code and a bit of refactoring * adding all multi-sample functionality; better output for novel alleles; parallel downloading for enterobase * small adjustment on a test * Fix c_jejuni_fastq_file filename in test * Adjusted kmer & vote numbers to match smaller test file. * Update conda recipe * Don't convert fasta_files paths to absolute paths (#23) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Relative paths in db (#25) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Fixed issue with scheme fasta loading during calling * Merge master into mentalist_v0.2 (#28) * new script to filter Mentalist flag symbols from the calls * Add .travis.yml file (#18) * Added travis.yml file * Added 'Build Status' badge * Update .travis.yml * Update requirements for TravisCI testing * kmer_class_for_locus function no longer exists * Don't test on OS X * Added coverage badge. * Updated macOS install instructions * Updated macOS install instructions * Update README.md * Update runtests.jl * TravisCI testing on v0.5 is broken. * Added <edam_operation> tag to 'mentalist call' galaxy tool (#21) * fixed a bug in the cgmlst download, fasta file decompression could be incorrect in some cases * adding import JSON; was not needed before because some other library was probably loading it, but for the tests we need this explicitly * new messages while loading a kmer db, better idea of how much each large step takes * lots of new unit tests and a new fastq testing file. Coverage should be much higher now. * Change version info for galaxy tools in master branch to 'master' * support for analysing multiple samples * reorganizing the argparse code and a bit of refactoring * adding all multi-sample functionality; better output for novel alleles; parallel downloading for enterobase * small adjustment on a test * Fix c_jejuni_fastq_file filename in test * Adjusted kmer & vote numbers to match smaller test file. * Update conda recipe * Don't convert fasta_files paths to absolute paths (#23) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Relative paths in db (#25) * Don't convert fasta_files paths to absolute paths * Prepend database directory path on to relative paths for allele fasta files in db * Don't create db_path variable, check for existence of fasta files * Tidy up newlines * Added test to check MLST calling after moving a database * Fixed issue with scheme fasta loading during calling * Updated galaxy tool * Removed newline * -s flag not supported * Updated git url in .shed.yml * Fork an unzip process to decompress downloaded cgMLST alleles (#30) * Fork an unzip process to decompress downloaded cgMLST alleles * Rewrite download_cgmlst_scheme() to handle new zip scheme files from cgmlst.org * Tidy up comments and fix total locus count * Fix test data filenames for L. pneumophila * Add unzip as a conda dependency * variable n_locus not used * Change conda version tag * Initial commit for db_info feature * Don't import calling_functions, create own db loading function * Add mentalist_version to db_info report * Use tab-separated output * Use HTTPS for cgmlst.org * Use full organism name in Galaxy Tool Data Table for Enterobase downloads (#61) * Update enterobase scheme download URL (#65) * Update enterobase scheme download URL * bump version number * Remove tests that count votes * Version bump
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Fixes #12.