| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/@wrapper_version@.galaxy1 |
| snpEff_get_chr_names |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| snpeff | 4.3.1t | package |
| gawk | 5.0.1 | package |
| Additional information about this tool |
snpEff -Xmx\${GALAXY_MEMORY_MB:-8192}m dump
#if $snpDb.genomeSrc == 'cached':
-dataDir ${snpDb.genomeVersion.fields.path}
$snpDb.genomeVersion
#elif $snpDb.genomeSrc == 'history':
-dataDir '${snpDb.snpeff_db.extra_files_path}'
'${snpDb.snpeff_db.metadata.genome_version}'
#elif $snpDb.genomeSrc == 'custom':
-dataDir '${snpDb.snpeff_db.extra_files_path}'
-configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}'
'${snpDb.snpeff_db.metadata.genome_version}'
#else
-dataDir "\$PWD/temp"
-download
'$snpDb.genome_version'
#end if
| awk '/# Chromosomes/{y=1;next}y' | grep "#" | grep -E "[0-9]" | awk 'BEGIN {err=1;} {c=$0;sub(/^[^a-zA-Z0-9_]+/, "", c) && err=0; sub(/[^a-zA-Z0-9_]+/, "\t", c) && err=0; sub(/[^0-9]*$/, "", c) && err=0; print c } END {exit err}' > '$chr_names'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
snpDb|genome_version: Bacillus_subtilis_subsp_subtilis_str_168 snpDb|genomeSrc: named |
name: value |
value |
| Test-2 |
snpDb|genome_version: should_not_match snpDb|genomeSrc: named |