| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/earlhaminst/gstf_preparation/gstf_preparation/0.4.3 (this tool) |
| toolshed.g2.bx.psu.edu/repos/earlhaminst/gstf_preparation/gstf_preparation/0.4.2 |
| toolshed.g2.bx.psu.edu/repos/earlhaminst/gstf_preparation/gstf_preparation/0.4.1 |
| toolshed.g2.bx.psu.edu/repos/earlhaminst/gstf_preparation/gstf_preparation/0.4.0 |
| toolshed.g2.bx.psu.edu/repos/earlhaminst/gstf_preparation/gstf_preparation/0.3.0 |
| gstf_preparation |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| python | 3.7 | package |
| Additional information about this tool |
python '$__tool_directory__/gstf_preparation.py'
#for $q in $queries
--gff3 '${q.genome}:${q.gff3_input}'
#end for
#if str($json) != 'None'
#for $v in $json
--json '$v'
#end for
#end if
#for $fasta_input in $fasta_inputs
--fasta '${fasta_input}'
#end for
#if $headers
--headers $headers
#end if
#if $filter
--filter $filter
#end if
#if $regions
--regions '$regions'
--ff '$filtered_fasta'
#end if
-o '$output_db'
--of '$output_fasta'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
queries_0|gff3_input: Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3 queries_0|genome: caenorhabditis_elegans fasta_inputs: Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa filter: coding headers: TranscriptId_species |
name: value name: value |
Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3 Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa value |
| Test-2 |
queries_0|gff3_input: Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3 queries_0|genome: caenorhabditis_elegans fasta_inputs: Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa filter: canonical headers: TranscriptId_species |
name: value name: value |
Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3 Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa value |
| Test-3 |
json: gene.json fasta_inputs: CDS.fasta filter: headers: |
name: value name: value |
gene.json CDS.fasta value |
| Test-4 |
json: gene.json fasta_inputs: CDS.fasta filter: coding headers: TranscriptId_species |
name: value name: value |
gene.json CDS.fasta value |
| Test-5 |
json: gene.json fasta_inputs: CDS.fasta filter: coding headers: TranscriptId_species regions: X |
name: value name: value name: value |
gene.json CDS.fasta value |
| Test-6 |
queries_0|gff3_input: MGP_PahariEiJ_G0008413.1.gff3 queries_0|genome: mus_pahari fasta_inputs: Mus_pahari.PAHARI_EIJ_v1.1.cds.all.shortened.fa filter: canonical headers: TranscriptId_species |
name: value name: value |
MGP_PahariEiJ_G0008413.1.gff3 Mus_pahari.PAHARI_EIJ_v1.1.cds.all.shortened.fa value |