| Previous changeset 24:cfcf33df7fc0 (2021-10-13) Next changeset 26:5b80f544c67f (2022-11-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3 |
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modified:
gbk2fa.py snpEff_create_db.xml snpEff_macros.xml |
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| diff -r cfcf33df7fc0 -r 5c7b70713fb5 gbk2fa.py --- a/gbk2fa.py Wed Oct 13 23:30:29 2021 +0000 +++ b/gbk2fa.py Wed Aug 03 16:33:45 2022 +0000 |
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| @@ -1,43 +1,47 @@ import argparse import bz2 -import contextlib import gzip -import sys -import magic from Bio import SeqIO -parser = argparse.ArgumentParser() -parser.add_argument("genbank_file", help="GenBank input file. Can be compressed with gzip or bzip2") -parser.add_argument("fasta_file", help="FASTA output datset") -parser.add_argument("--remove_version", dest="remove_version", action="store_true", help="Remove version number from NCBI form formatted accession numbers. For example, this would convert 'B000657.2' to 'B000657'") -args = parser.parse_args() -gbk_filename = args.genbank_file -fa_filename = args.fasta_file +def get_opener(gbk_filename): + try: + bz2.open(gbk_filename).read(1) + return bz2.open + except OSError: + pass + try: + gzip.open(gbk_filename).read(1) + return gzip.open + except OSError: + return open -@contextlib.contextmanager -def get_file_handle(gbk_filename): - f_type = magic.from_file(args.genbank_file, mime=True) - if f_type == 'text/plain': - input_handle = open(gbk_filename, "r") - elif f_type == 'application/gzip' or f_type == 'application/x-gzip': - input_handle = gzip.open(gbk_filename, "rt") - elif f_type == 'application/x-bzip2': - input_handle = bz2.open(gbk_filename, "rt") - else: - sys.exit("Cannot process file of type {}. Only plain, gzip'ed, and bzip2'ed genbank files are accepted ".format(f_type)) - yield input_handle - input_handle.close() +parser = argparse.ArgumentParser() +parser.add_argument( + "genbank_file", + help="GenBank input file. Can be compressed with gzip or bzip2" +) +parser.add_argument( + "fasta_file", help="FASTA output datset" +) +parser.add_argument( + "--remove_version", action="store_true", + help="Remove version number from NCBI form formatted accession numbers. " + "For example, this would convert 'B000657.2' to 'B000657'" +) +args = parser.parse_args() -with get_file_handle(gbk_filename) as input_handle, open(fa_filename, "w") as output_handle: - - for seq_record in SeqIO.parse(input_handle, "genbank"): +gbk_open = get_opener(args.genbank_file) +with gbk_open(args.genbank_file, 'rt') as input_handle, \ + open(args.fasta_file, 'w') as output_handle: + for seq_record in SeqIO.parse(input_handle, 'genbank'): if args.remove_version: seq_id = seq_record.id.split('.')[0] else: seq_id = seq_record.id print('Writing FASTA record: {}'.format(seq_id)) - output_handle.write(">{}\n{}\n".format(seq_id, seq_record.seq)) + print('>' + seq_id, file=output_handle) + print(seq_record.seq, file=output_handle) |
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| diff -r cfcf33df7fc0 -r 5c7b70713fb5 snpEff_create_db.xml --- a/snpEff_create_db.xml Wed Oct 13 23:30:29 2021 +0000 +++ b/snpEff_create_db.xml Wed Aug 03 16:33:45 2022 +0000 |
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| b'@@ -1,77 +1,66 @@\n-<tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy4">\n+<tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy5">\n <description> database from Genbank or GFF record</description>\n <macros>\n <import>snpEff_macros.xml</import>\n </macros>\n <requirements>\n <expand macro="requirement" />\n- <requirement type="package" version="3.6">python</requirement>\n- <requirement type="package" version="1.70">biopython</requirement>\n- <requirement type="package" version="0.4.15">python-magic</requirement>\n- <requirement type="package" version="5.32">libmagic</requirement>\n+ <requirement type="package" version="1.79">biopython</requirement>\n </requirements>\n <expand macro="stdio" />\n <expand macro="version_command" />\n <command><![CDATA[\n- #if str( $input_type.input_type_selector ) == "gb":\n- #if str( $input_type.fasta ) == "yes":\n- python3 \'$__tool_directory__/gbk2fa.py\' \'${input_type.input_gbk}\' \'${output_fasta}\'\n- #if $input_type.remove_version:\n- \'${input_type.remove_version}\'\n- #end if\n- &&\n- #end if\n+ #if str($input_type.input_type_selector) == "gb" and str($input_type.fasta) == "yes":\n+ python3 \'$__tool_directory__/gbk2fa.py\' \'${input_type.input}\' \'${output_fasta}\' ${input_type.remove_version} &&\n #end if\n \n mkdir -p \'${snpeff_output.files_path}\'/\'${genome_version}\' &&\n \n- #if str( $input_type.input_type_selector ) == "gb":\n- #if $input_type.input_gbk.is_of_type("genbank"):\n- ln -s \'${input_type.input_gbk}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/genes.gbk &&\n- #elif $input_type.input_gbk.is_of_type("genbank.gz"):\n- ln -s \'${input_type.input_gbk}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/genes.gbk.gz &&\n+ #if str($input_type.input_type_selector) == "gb":\n+ #if $input_type.input.is_of_type("genbank"):\n+ ln -s \'${input_type.input}\' \'${snpeff_output.files_path}/${genome_version}/genes.gbk\' &&\n+ #elif $input_type.input.is_of_type("genbank.gz"):\n+ ln -s \'${input_type.input}\' \'${snpeff_output.files_path}/${genome_version}/genes.gbk.gz\' &&\n #end if\n- #elif str( $input_type.input_type_selector ) == "gff":\n-\t #if $input_type.reference_source.reference_source_selector == "history":\n-\t\t\t #if $input_type.reference_source.input_fasta.is_of_type("fasta"):\n- ln -s \'${input_type.reference_source.input_fasta}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/sequences.fa &&\n-\t #elif $input_type.reference_source.input_fasta.is_of_type("fasta.gz"):\n-\t ln -s \'${input_type.reference_source.input_fasta}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/sequences.fa.gz &&\n-\t #end if\n-\t\t\t#elif $input_type.reference_source.reference_source_selector == "cached":\n-\t\t\t ln -s \'${input_type.reference_source.ref_file.fields.path}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/sequences.fa &&\n-\t\t\t#end if\n- ln -s \'${input_type.input_gff}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/genes.gff &&\n- #elif str( $input_type.input_type_selector ) == "gtf":\n-\t #if $input_type.reference_source.reference_source_selector == "history":\n-\t\t\t #if $input_type.reference_source.input_fasta.is_of_type("fasta"):\n- ln -s \'${input_type.reference_source.input_fasta}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/sequences.fa &&\n-\t #elif $input_type.reference_source.input_fasta.is_of_type("fasta.gz"):\n-\t ln -s \'${input_type.reference_source.input_fasta}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/sequences.fa.gz &&\n-\t #end if\n-\t\t\t#elif $input_type.reference_source.reference_source_sele'..b'</when>\n-\t\t </conditional>\n+ <param name="input" type="data" format="gff3" label="GFF dataset to build database from" help="This GFF file will be used to generate snpEff database"/>\n+ <expand macro="ref_select" />\n </when>\n <when value="gtf">\n- <param name="input_gtf" type="data" format="gtf" label="GTF dataset to build database from" help="This GTF file will be used to generate snpEff database"/>\n- <conditional name="reference_source">\n-\t\t <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">\n-\t\t <option value="cached">Locally cached</option>\n-\t\t <option value="history">History</option>\n-\t\t </param>\n-\t\t <when value="cached">\n-\t\t <param name="ref_file" type="select" label="Select reference genome">\n-\t\t <options from_data_table="fasta_indexes"/>\n-\t\t </param>\n-\t\t </when>\n-\t\t <when value="history"> \n-\t\t <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Genome in FASTA format" help="This dataset is required for generating SnpEff database. See help section below."/>\n-\t\t </when>\n-\t\t </conditional>\n+ <param name="input" type="data" format="gtf" label="GTF dataset to build database from" help="This GTF file will be used to generate snpEff database"/>\n+ <expand macro="ref_select" />\n </when>\n </conditional>\n <param name="codon_table" type="select" label="Select genetic code for this sequence" help="If this sequence uses non-standard genetic code, select one from these options">\n@@ -162,7 +125,7 @@\n <test>\n <param name="genome_version" value="pBR322"/>\n <param name="input_type_selector" value="gb"/>\n- <param name="input_gbk" value="pBR322.gbk" />\n+ <param name="input" value="pBR322.gbk" />\n <output name="snpeff_output">\n <assert_contents>\n <has_text text="pBR322" />\n@@ -173,7 +136,7 @@\n <test>\n <param name="genome_version" value="pBR322"/>\n <param name="input_type_selector" value="gb"/>\n- <param name="input_gbk" value="pBR322.gbk.gz" />\n+ <param name="input" value="pBR322.gbk.gz" />\n <output name="snpeff_output">\n <assert_contents>\n <has_text text="pBR322" />\n@@ -186,7 +149,7 @@\n <param name="input_type_selector" value="gff"/>\n <param name="reference_source_selector" value="history"/>\n <param name="input_fasta" value="pBR322_test2.fna" />\n- <param name="input_gff" value="pBR322.gff3"/>\n+ <param name="input" value="pBR322.gff3"/>\n <output name="snpeff_output">\n <assert_contents>\n <has_text text="pBR322" />\n@@ -198,7 +161,7 @@\n <param name="input_type_selector" value="gff"/>\n <param name="reference_source_selector" value="history"/>\n <param name="input_fasta" value="pBR322_test2.fna.gz" />\n- <param name="input_gff" value="pBR322.gff3"/>\n+ <param name="input" value="pBR322.gff3"/>\n <output name="snpeff_output">\n <assert_contents>\n <has_text text="pBR322" />\n@@ -210,7 +173,7 @@\n <param name="input_type_selector" value="gtf"/>\n <param name="reference_source_selector" value="history"/>\n <param name="input_fasta" value="Saccharomyces_mito.fa.gz" />\n- <param name="input_gtf" value="Saccharomyces_mito.gtf" />\n+ <param name="input" value="Saccharomyces_mito.gtf" />\n <output name="snpeff_output">\n <assert_contents>\n <has_text text="Saccharomyces_mito" />\n' |
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| diff -r cfcf33df7fc0 -r 5c7b70713fb5 snpEff_macros.xml --- a/snpEff_macros.xml Wed Oct 13 23:30:29 2021 +0000 +++ b/snpEff_macros.xml Wed Aug 03 16:33:45 2022 +0000 |
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| @@ -18,6 +18,22 @@ <token name="@SNPEFF_VERSION@">SnpEff4.3</token> <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token> <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token> + <xml name="ref_select"> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Select reference genome"> + <options from_data_table="fasta_indexes"/> + </param> + </when> + <when value="history"> + <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Genome in FASTA format" help="This dataset is required for generating SnpEff database. See help section below."/> + </when> + </conditional> + </xml> <token name="@EXTERNAL_DOCUMENTATION@"> |