| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.1.0 |
| snpSift_extractFields |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| snpsift | 4.3.1t | package |
| coreutils | 8.25 | package |
| perl | 5.26 | package |
| Additional information about this tool |
if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi &&
cat '${input}'
#if $one_effect_per_line:
| perl "\$SNPSIFT_JAR_PATH/scripts/vcfEffOnePerLine.pl"
#end if
| SnpSift -Xmx6G extractFields
#if $separator:
-s '${separator}'
#end if
#if $empty_text:
-e '${empty_text}'
#end if
-
#echo ' '.join(['"%s"' % x for x in $extract.split()])
> '${output}'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: test_rmInfo.vcf extract: CHROM POS REF ALT EFF[*].EFFECT |
name: value |
test_rmInfo.vcf value |
| Test-2 |
input: test_rmInfo.vcf extract: CHROM POS REF ALT EFF[*].EFFECT separator: , |
name: value |
test_rmInfo.vcf value |
| Test-3 |
input: extFields_test3_in.vcf extract: CHROM POS ID REF ALT FILTER ANN[*].EFFECT one_effect_per_line: True |
name: value |
extFields_test3_in.vcf value |