| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/smgu_frameshift_deletions_checks/smgu_frameshift_deletions_checks/0.5.2+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/smgu_frameshift_deletions_checks/smgu_frameshift_deletions_checks/0.5.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/smgu_frameshift_deletions_checks/smgu_frameshift_deletions_checks/0.5.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/smgu_frameshift_deletions_checks/smgu_frameshift_deletions_checks/0.4.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/smgu_frameshift_deletions_checks/smgu_frameshift_deletions_checks/0.4.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/smgu_frameshift_deletions_checks/smgu_frameshift_deletions_checks/0.3.9+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/smgu_frameshift_deletions_checks/smgu_frameshift_deletions_checks/0.3.9+galaxy0 |
| smgu_frameshift_deletions_checks |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| smallgenomeutilities | 0.5.2 | package |
| Additional information about this tool |
#if $input.is_of_type("cram"):
ln -s '$input' input.cram &&
ln -s '$input.metadata.cram_index' input.cram.crai &&
#elif $input.is_of_type("bam"):
ln -s '$input' input.bam &&
ln -s '$input.metadata.bam_index' input.bam.bai &&
#else:
# raise TypeError('Unknown input alignment type ${input.ext}')
#end if
ln -s '$consensus' consensus.fasta &&
#if str($ref_data.choice) == 'custom':
ln -s '$reference' reference.fa &&
#else:
ln -s '$__tool_directory__/ref_NC_045512.2.fasta' reference.fa &&
#end if
frameshift_deletions_checks
--input=input.${input.ext}
--consensus=consensus.fasta
--reference=reference.fa
#if str($align_data.choice) == 'chain':
--chain='$align_data.chain'
#end if
#if str($ref_data.choice) == 'standard':
--genes='$__tool_directory__'/annotations_NC_045512.2.gff3
--orf1ab='cds-YP_009724389.1'
#else:
--genes='$ref_data.genes'
--orf1ab='$ref_data.orf1ab'
#end if
$out_options.english
$out_options.zero_based
--output=report.tsv &&
python '$__tool_directory__/frameshift_deletions_report_fixer.py' report.tsv '$report'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
consensus: consensus.bcftools.fasta.gz input: REF_aln_trim.cram align_data|choice: mafft ref_data|choice: standard |
name: value |
consensus.bcftools.fasta.gz REF_aln_trim.cram value |
| Test-2 |
consensus: consensus.bcftools_nogap.fasta.gz input: REF_aln_trim.cram align_data|chain: consensus.bcftools_nogap.chain align_data|choice: chain ref_data|choice: standard |
name: value |
consensus.bcftools_nogap.fasta.gz REF_aln_trim.cram consensus.bcftools_nogap.chain value |
| Test-3 |
consensus: consensus.bcftools.fasta.gz input: REF_aln_trim.cram align_data|chain: consensus.bcftools.chain align_data|choice: chain ref_data|choice: standard |
name: value |
consensus.bcftools.fasta.gz REF_aln_trim.cram consensus.bcftools.chain value |
| Test-4 |
consensus: consensus.bcftools.fasta.gz input: REF_aln_trim.cram align_data|chain: consensus.bcftools.chain align_data|choice: chain ref_data|choice: standard out_options|english: False |
name: value |
consensus.bcftools.fasta.gz REF_aln_trim.cram consensus.bcftools.chain value |
| Test-5 |
consensus: consensus.bcftools.fasta.gz input: REF_aln_trim.cram align_data|chain: consensus.bcftools.chain align_data|choice: chain ref_data|reference: NC_045512.2.fasta ref_data|genes: Genes_NC_045512.2.GFF3 ref_data|choice: custom |
name: value |
consensus.bcftools.fasta.gz REF_aln_trim.cram consensus.bcftools.chain NC_045512.2.fasta Genes_NC_045512.2.GFF3 value |