| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4 |
| toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy3 |
| toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3.1t.1 |
| snpEff_build_gb |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| snpeff | 4.3.1t | package |
| biopython | 1.79 | package |
| Additional information about this tool |
#if str($input_type.input_type_selector) == "gb" and str($input_type.fasta) == "yes":
python3 '$__tool_directory__/gbk2fa.py' '${input_type.input}' '${output_fasta}' ${input_type.remove_version} &&
#end if
mkdir -p '${snpeff_output.files_path}'/'${genome_version}' &&
#if str($input_type.input_type_selector) == "gb":
#if $input_type.input.is_of_type("genbank"):
ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.gbk' &&
#elif $input_type.input.is_of_type("genbank.gz"):
ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.gbk.gz' &&
#end if
#else:
#if $input_type.reference_source.reference_source_selector == "history":
#if $input_type.reference_source.input_fasta.is_of_type("fasta"):
ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}/${genome_version}/sequences.fa' &&
#elif $input_type.reference_source.input_fasta.is_of_type("fasta.gz"):
ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}/${genome_version}/sequences.fa.gz' &&
#end if
#elif $input_type.reference_source.reference_source_selector == "cached":
ln -s '${input_type.reference_source.ref_file.fields.path}' '${snpeff_output.files_path}/${genome_version}/sequences.fa' &&
#end if
ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.${input_type.input_type_selector}' &&
#end if
snpEff -Xmx\${GALAXY_MEMORY_MB:-8192}m build -v
-configOption '${genome_version}'.genome='${genome_version}'
-configOption '${genome_version}'.codonTable='${codon_table}'
#if str($input_type.input_type_selector) == "gb":
-genbank
#elif str($input_type.input_type_selector) == "gff":
-gff3
#elif str($input_type.input_type_selector) == "gtf":
-gtf22
#end if
-dataDir '${snpeff_output.files_path}' '${genome_version}' &&
echo '${genome_version}.genome : ${genome_version}' >> '${snpeff_output.files_path}'/snpEff.config &&
echo '${genome_version}.codonTable : ${codon_table}' >> '${snpeff_output.files_path}'/snpEff.config
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
genome_version: pBR322 input_type|input: pBR322.gbk input_type|input_type_selector: gb |
name: value name: value |
pBR322.gbk value |
| Test-2 |
genome_version: pBR322 input_type|input: pBR322.gbk.gz input_type|input_type_selector: gb |
name: value name: value |
pBR322.gbk.gz value |
| Test-3 |
genome_version: pBR322 input_type|input: pBR322.gff3 input_type|reference_source|input_fasta: pBR322_test2.fna input_type|reference_source|reference_source_selector: history input_type|input_type_selector: gff |
name: value |
pBR322.gff3 pBR322_test2.fna value |
| Test-4 |
genome_version: pBR322 input_type|input: pBR322.gff3 input_type|reference_source|input_fasta: pBR322_test2.fna.gz input_type|reference_source|reference_source_selector: history input_type|input_type_selector: gff |
name: value |
pBR322.gff3 pBR322_test2.fna.gz value |
| Test-5 |
genome_version: Saccharomyces_mito input_type|input: Saccharomyces_mito.gtf input_type|reference_source|input_fasta: Saccharomyces_mito.fa.gz input_type|reference_source|reference_source_selector: history input_type|input_type_selector: gtf |
name: value |
Saccharomyces_mito.gtf Saccharomyces_mito.fa.gz value |