Galaxy | CPT Public | Accessible Workflow | PAP 2018 Functional (v8.15)

PAP 2018 Functional (v8.15)

Annotation: Functional Annotation Workflow: Must have Apollo data to run. Updated to 2018 versions of NCBI, Uniprot, and CPT Canonical Phage BLAST databases

Step	Annotation
Step 1: Input dataset input select at runtime
Step 2: Input dataset input select at runtime
Step 3: Input dataset input select at runtime
Step 4: Remove Description Fasta file Output dataset 'output' from step 1
Step 5: Unknown Tool with id 'edu.tamu.cpt2.webapollo.fetch_jbrowse'
Step 6: Unknown Tool with id 'edu.tamu.cpt2.cacao.add_org'
Step 7: Reformat GFF3 File GFF3 Annotations Output dataset 'output' from step 3
Step 8: Get open reading frames (ORFs) or coding sequences (CDSs) Sequence file (nucleotides) Output dataset 'out' from step 4 Genetic code 11. Bacterial Look for ORFs or CDSs Look for ORFs (check for stop codons only, ignore start codons) Minimum length ORF/CDS (in amino acids, e.g. 30 aa = 90 bp plus any stop codon) 30 Strand to search Search both the forward and reverse strand
Step 9: NCBI BLAST+ blastn Nucleotide query sequence(s) Output dataset 'out' from step 4 Subject database/sequences Locally installed BLAST database Nucleotide BLAST database nt_2018.9 None Empty. None Empty. Type of BLAST dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences Set expectation value cutoff 0.001 Output format Tabular (extended 25 columns) Advanced Options Hide Advanced Options
Step 10: GFF3 Feature Sequence Export Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 4 GFF3 Annotations Output dataset 'default' from step 7 Filter for specific feature types CDS Remove description (use if blasting) False
Step 11: Unknown Tool with id 'edu.tamu.cpt2.phage.fsfinder'
Step 12: GFF3 Add Gene to CDS GFF3 Annotations Output dataset 'out_gff3_file' from step 8
Step 13: Blast Tabular Dice Filter Blast Results Output dataset 'output1' from step 9 Minimum dice score 0.2
Step 14: Start Codon Statistics Fasta file Output dataset 'default' from step 10
Step 15: Stop Codon Statistics Fasta file Output dataset 'default' from step 10
Step 16: Fasta Translate Fasta file Output dataset 'default' from step 10 Target output Protein Translation table to use [11] The Bacterial, Archaeal and Plant Plastid Code Remove stop characters True Convert first residue to Met False
Step 17: GFF3 Filter: Require Phage Start Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 4 GFF3 Annotations Output dataset 'output' from step 12
Step 18: BlastN TSV to gapped GFF3 Blast Results Output dataset 'output' from step 13 Gap Size 10
Step 19: TMHMM (GFF3) Protein Fasta file Output dataset 'default' from step 16
Step 20: Unknown Tool with id 'interproscan-5.22'
Step 21: NCBI BLAST+ blastp Protein query sequence(s) Output dataset 'default' from step 16 Subject database/sequences Locally installed BLAST database Protein BLAST database nr_2018.9 None Empty. None Empty. Type of BLAST blastp - Traditional BLASTP to compare a protein query to a protein database Set expectation value cutoff 0.001 Output format BLAST XML Advanced Options Hide Advanced Options
Step 22: NCBI BLAST+ blastp Protein query sequence(s) Output dataset 'default' from step 16 Subject database/sequences Locally installed BLAST database Protein BLAST database trembl_2018.9 None Empty. None Empty. Type of BLAST blastp - Traditional BLASTP to compare a protein query to a protein database Set expectation value cutoff 0.001 Output format BLAST XML Advanced Options Hide Advanced Options
Step 23: NCBI BLAST+ blastp Protein query sequence(s) Output dataset 'default' from step 16 Subject database/sequences Locally installed BLAST database Protein BLAST database sprot_2018.9 None Empty. None Empty. Type of BLAST blastp - Traditional BLASTP to compare a protein query to a protein database Set expectation value cutoff 0.001 Output format BLAST XML Advanced Options Hide Advanced Options
Step 24: NCBI BLAST+ blastp Protein query sequence(s) Output dataset 'default' from step 16 Subject database/sequences Locally installed BLAST database Protein BLAST database canonical_prot_2018.9 None Empty. None Empty. Type of BLAST blastp - Traditional BLASTP to compare a protein query to a protein database Set expectation value cutoff 0.001 Output format BLAST XML Advanced Options Hide Advanced Options
Step 25: Gff3 Filter: Require SD Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 4 GFF3 Annotations Output dataset 'stdout' from step 17
Step 26: Rebase GFF3 features Parent GFF3 annotations Output dataset 'default' from step 7 Child GFF3 annotations to rebase against parent Output dataset 'output' from step 19 Interpro specific modifications False Map protein translated results to original DNA data True Mapping Key ID
Step 27: Rebase Wig Analysis Results Parent GFF3 annotations Output dataset 'default' from step 7 Wig Results Output dataset 'bw_i' from step 19 Map protein translated results to original DNA data True Mapping Key ID
Step 28: Rebase Wig Analysis Results Parent GFF3 annotations Output dataset 'default' from step 7 Wig Results Output dataset 'bw_o' from step 19 Map protein translated results to original DNA data True Mapping Key ID
Step 29: Rebase Wig Analysis Results Parent GFF3 annotations Output dataset 'default' from step 7 Wig Results Output dataset 'bw_m' from step 19 Map protein translated results to original DNA data True Mapping Key ID
Step 30: Rebase GFF3 features Parent GFF3 annotations Output dataset 'default' from step 7 Child GFF3 annotations to rebase against parent Output dataset 'output_gff3' from step 20 Interpro specific modifications True Map protein translated results to original DNA data True Mapping Key ID
Step 31: Interrupted gene detection tool GFF3 Annotations Output dataset 'default' from step 7 Blastp Results Output dataset 'output1' from step 21 Separation Minimum -1 No value found for 'Separation Minimum'. Using default: '-1'. Separation Maximum 10000 No value found for 'Separation Maximum'. Using default: '10000'. Percent Identity Threshold 0.3 No value found for 'Percent Identity Threshold'. Using default: '0.3'.
Step 32: BlastXML to gapped GFF3 Blast Results Output dataset 'output1' from step 21 Gap Size 10 Trim sides of blast hits Trim start and end Include protein alignment in Blast view in Apollo/JBrowse True
Step 33: BlastXML to gapped GFF3 Blast Results Output dataset 'output1' from step 22 Gap Size 10 Trim sides of blast hits Trim start and end Include protein alignment in Blast view in Apollo/JBrowse True
Step 34: BlastXML to gapped GFF3 Blast Results Output dataset 'output1' from step 23 Gap Size 10 Trim sides of blast hits Trim start and end Include protein alignment in Blast view in Apollo/JBrowse True
Step 35: BlastXML to gapped GFF3 Blast Results Output dataset 'output1' from step 24 Gap Size 10 Trim sides of blast hits Trim only end Include protein alignment in Blast view in Apollo/JBrowse True
Step 36: GFF3 Feature Sequence Export Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 4 GFF3 Annotations Output dataset 'stdout' from step 25 Filter for specific feature types CDS Remove description (use if blasting) True
Step 37: Identify Lipoboxes Naive orf calls Output dataset 'stdout' from step 25 Genome Output dataset 'out' from step 4 Minimum distance in codons to start of lipobox 10 Maximum distance in codons to start of lipobox 60
Step 38: Wig to BigWig Wig File Output dataset 'output' from step 27 Fasta File Output dataset 'out' from step 4
Step 39: Wig to BigWig Wig File Output dataset 'output' from step 28 Fasta File Output dataset 'out' from step 4
Step 40: Wig to BigWig Wig File Output dataset 'output' from step 29 Fasta File Output dataset 'out' from step 4
Step 41: Rebase GFF3 features Parent GFF3 annotations Output dataset 'default' from step 7 Child GFF3 annotations to rebase against parent Output dataset 'output' from step 32 Interpro specific modifications False Map protein translated results to original DNA data True Mapping Key ID
Step 42: Rebase GFF3 features Parent GFF3 annotations Output dataset 'default' from step 7 Child GFF3 annotations to rebase against parent Output dataset 'output' from step 33 Interpro specific modifications False Map protein translated results to original DNA data True Mapping Key ID
Step 43: Rebase GFF3 features Parent GFF3 annotations Output dataset 'default' from step 7 Child GFF3 annotations to rebase against parent Output dataset 'output' from step 34 Interpro specific modifications False Map protein translated results to original DNA data True Mapping Key ID
Step 44: Rebase GFF3 features Parent GFF3 annotations Output dataset 'default' from step 7 Child GFF3 annotations to rebase against parent Output dataset 'output' from step 35 Interpro specific modifications False Map protein translated results to original DNA data True Mapping Key ID
Step 45: Fasta Translate Fasta file Output dataset 'default' from step 36 Target output Protein Translation table to use [11] The Bacterial, Archaeal and Plant Plastid Code Remove stop characters True Convert first residue to Met False
Step 46: TMHMM (GFF3) Protein Fasta file Output dataset 'default' from step 45
Step 47: NCBI BLAST+ blastp Protein query sequence(s) Output dataset 'default' from step 45 Subject database/sequences Locally installed BLAST database Protein BLAST database nr_2019.6 None Empty. None Empty. Type of BLAST blastp - Traditional BLASTP to compare a protein query to a protein database Set expectation value cutoff 0.001 Output format BLAST XML Advanced Options Hide Advanced Options
Step 48: Rebase GFF3 features Parent GFF3 annotations Output dataset 'stdout' from step 25 Child GFF3 annotations to rebase against parent Output dataset 'output' from step 46 Interpro specific modifications False Map protein translated results to original DNA data True Mapping Key ID
Step 49: Intersect GFF3 Annotations A Output dataset 'default' from step 48 GFF3 Annotations B Output dataset 'default' from step 37
Step 50: Remove Annotation Feature GFF3 Annotations Output dataset 'oa' from step 49 Remove 'remark' features True Remove 'region' features True No value found for 'Remove 'region' features'. Using default: 'True'.
Step 51: Remove Annotation Feature GFF3 Annotations Output dataset 'ob' from step 49 Remove 'remark' features True Remove 'region' features True No value found for 'Remove 'region' features'. Using default: 'True'.
Step 52: Unknown Tool with id 'jbrowse-cpt'
Step 53: Unknown Tool with id 'edu.tamu.cpt2.webapollo.create_or_update'
Step 54: Unknown Tool with id 'edu.tamu.cpt2.webapollo.iframe'

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cory-maughmer

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PAP 2018 Functional (v8.15)

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