| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.2.2+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.2.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.1.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.0.1.0 |
| trinotate |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| trinotate | 3.2.2 | package |
| gnu-wget | 1.18 | package |
| Additional information about this tool |
#if str($cond_download.select_download) == "yes":
Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate &&
#else:
ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite &&
#end if
Trinotate Trinotate.sqlite init --gene_trans_map '$gene_trans_map' --transcript_fasta $trinity --transdecoder_pep '$transdecoder' &&
#if $blastp:
Trinotate Trinotate.sqlite LOAD_swissprot_blastp '$blastp' &&
#end if
#if $blastx:
Trinotate Trinotate.sqlite LOAD_swissprot_blastx '$blastx' &&
#end if
#if $hmmscan:
Trinotate Trinotate.sqlite LOAD_pfam '$hmmscan' &&
#end if
#if $tmhmm:
Trinotate Trinotate.sqlite LOAD_tmhmm '$tmhmm' &&
#end if
#if $signalp:
Trinotate Trinotate.sqlite LOAD_signalp '$signalp' &&
#end if
Trinotate Trinotate.sqlite report -E $report_option.E --pfam_cutoff $report_option.pfam_cutoff $report_option.incl_pep $report_option.incl_trans > '$trinotate_out'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
trinity: Trinity.fasta transdecoder: Trinity.fasta.transdecoder.pep gene_trans_map: Trinity.fasta.gene_to_trans_map blastp: swissprot.blastp.outfmt6 blastx: swissprot.blastx.outfmt6 hmmscan: TrinotatePFAM.out tmhmm: tmhmm.out signalp: signalp.out |
name: value |
Trinity.fasta Trinity.fasta.transdecoder.pep Trinity.fasta.gene_to_trans_map swissprot.blastp.outfmt6 swissprot.blastx.outfmt6 TrinotatePFAM.out tmhmm.out signalp.out value |
| Test-2 |
trinity: Trinity.fasta transdecoder: Trinity.fasta.transdecoder.pep gene_trans_map: Trinity.fasta.gene_to_trans_map blastp: swissprot.blastp.outfmt6 blastx: swissprot.blastx.outfmt6 hmmscan: TrinotatePFAM.out report_option|incl_pep: True report_option|incl_trans: True keep_sqlite: True |
name: value |
Trinity.fasta Trinity.fasta.transdecoder.pep Trinity.fasta.gene_to_trans_map swissprot.blastp.outfmt6 swissprot.blastx.outfmt6 TrinotatePFAM.out value |