| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.4+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.4+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy6 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy5 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy4 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.0.1+galaxy0 |
| ivar_trim |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| ivar | 1.4.4 | package |
| python | 3.11.9 | package |
| samtools | 1.21 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_bam: covid19/PC00101P_sub.sorted.bam primer|input_bed: covid19/ARTIC-V1.bed inc_primers: True trimmed_length|min_len: 30 trimmed_length|filter: custom |
name: value |
covid19/PC00101P_sub.sorted.bam covid19/ARTIC-V1.bed value |
| Test-2 |
input_bam: covid19/PC00101P_sub.sorted.bam primer|input_bed: covid19/ARTIC-V1-bad.bed inc_primers: True trimmed_length|min_len: 30 trimmed_length|filter: custom |
name: value |
covid19/PC00101P_sub.sorted.bam covid19/ARTIC-V1-bad.bed value |
| Test-3 |
input_bam: zika/Z52_a.sorted.bam primer|input_bed: zika/db/zika_primers.bed primer|source: history trimmed_length|min_len: 30 trimmed_length|filter: custom |
name: value |
zika/Z52_a.sorted.bam zika/db/zika_primers.bed value |
| Test-4 |
input_bam: zika/Z52_b.sorted.bam primer|input_bed: zika/db/zika_primers.bed primer|source: history trimmed_length|filter: auto |
name: value |
zika/Z52_b.sorted.bam zika/db/zika_primers.bed value |
| Test-5 |
input_bam: sars-cov-2/sars_cov2_untrimmed.bam primer|cached_bed: SARS-CoV-2-ARTICv1 primer|source: cached trimmed_length|min_len: 30 trimmed_length|filter: custom |
name: value |
sars-cov-2/sars_cov2_untrimmed.bam value |
| Test-6 |
input_bam: sars-cov-2/sars_cov2_untrimmed.bam primer|cached_bed: SARS-CoV-2-ARTICv1 primer|source: cached amplicons|filter_by: yes_compute trimmed_length|min_len: 30 trimmed_length|filter: custom |
name: value |
sars-cov-2/sars_cov2_untrimmed.bam value |