| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.2+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy4 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.0.1+galaxy0 |
| ivar_removereads |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| ivar | 1.3.2 | package |
| python | 3.10.8 | package |
| samtools | 1.16.1 | package |
| Additional information about this tool |
cp '$input_bed' binding_sites.bed &&
python '$__tool_directory__/sanitize_bed.py' binding_sites.bed &&
#if $amplicons.computed == "yes"
python '$__tool_directory__/write_amplicon_info_file.py' binding_sites.bed amplicon_info.tsv &&
#else
ln -s '$amplicon_info' amplicon_info.tsv &&
#end if
ivar getmasked
-i '$variants_tsv' -b binding_sites.bed -f amplicon_info.tsv -p masked_primers &&
python '$__tool_directory__/completemask.py' masked_primers.txt amplicon_info.tsv &&
ln -s '$input_bam' sorted.bam &&
ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&
ivar removereads
-i sorted.bam
-b binding_sites.bed
-p removed_reads.bam
-t masked_primers.txt
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_bam: zika/Z52_a.trimmed.sorted.bam variants_tsv: zika/primers_Z52_consensus.tsv input_bed: zika/db/zika_primers_consensus.bed amplicons|amplicon_info: zika/db/pair_information.tsv amplicons|computed: no |
name: value |
zika/Z52_a.trimmed.sorted.bam zika/primers_Z52_consensus.tsv zika/db/zika_primers_consensus.bed zika/db/pair_information.tsv value |
| Test-2 |
input_bam: zika/Z52_a.trimmed.sorted.bam variants_tsv: zika/primers_Z52_consensus.tsv input_bed: zika/db/zika_primers_consensus.bed amplicons|computed: yes |
name: value |
zika/Z52_a.trimmed.sorted.bam zika/primers_Z52_consensus.tsv zika/db/zika_primers_consensus.bed value |