| Previous changeset 11:dbe37a658cd2 (2020-09-27) Next changeset 13:51a7a2a82902 (2020-10-06) |
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Commit message:
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 4579d0c461c30183a3092d84013e30f53f072ca1-dirty" |
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modified:
gstf_preparation.py gstf_preparation.xml |
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| diff -r dbe37a658cd2 -r 99bae410128c gstf_preparation.py --- a/gstf_preparation.py Sun Sep 27 18:54:31 2020 +0000 +++ b/gstf_preparation.py Mon Oct 05 13:33:59 2020 +0000 |
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| @@ -258,7 +258,7 @@ if gene is None: # This can happen when loading a JSON file from Ensembl continue - if 'confidence' in gene and gene['confidence'] != 'high': + if 'confidence' in gene and gene['confidence'].lower() != 'high': print("Gene %s has confidence %s (not high), discarding" % (gene['id'], gene['confidence']), file=sys.stderr) continue gene_id = gene['id'] @@ -300,7 +300,7 @@ parser.add_option('--fasta', action='append', default=[], help='Path of the input FASTA files') parser.add_option('--filter', type='choice', choices=['canonical', 'coding', ''], default='', help='Which transcripts to keep') parser.add_option('--headers', type='choice', - choices=['TranscriptId_species', 'GeneSymbol-TranscriptID_species', 'TranscriptSymbol-TranscriptID_species', ''], + choices=['TranscriptId_species', 'TranscriptID-GeneSymbol_species', 'TranscriptID-TranscriptSymbol_species', ''], default='', help='Change the header line of the FASTA sequences to this format') parser.add_option('--regions', default="", help='Comma-separated list of region IDs for which FASTA sequences should be filtered') parser.add_option('-o', '--output', help='Path of the output SQLite file') @@ -454,12 +454,12 @@ # Change the FASTA header to '>TranscriptId_species', as required by TreeBest # Remove any underscore in the species entry.header = ">%s_%s" % (transcript_id, transcript['species'].replace('_', '')) - elif options.headers == "GeneSymbol-TranscriptID_species": + elif options.headers == "TranscriptID-GeneSymbol_species": # Remove any underscore in the species - entry.header = ">%s-%s_%s" % (transcript['gene_symbol'], transcript_id, transcript['species'].replace('_', '')) - elif options.headers == "TranscriptSymbol-TranscriptID_species": + entry.header = ">%s-%s_%s" % (transcript_id, transcript['gene_symbol'], transcript['species'].replace('_', '')) + elif options.headers == "TranscriptID-TranscriptSymbol_species": # Remove any underscore in the species - entry.header = ">%s-%s_%s" % (transcript['transcript_symbol'], transcript_id, transcript['species'].replace('_', '')) + entry.header = ">%s-%s_%s" % (transcript_id, transcript['transcript_symbol'], transcript['species'].replace('_', '')) if transcript['seq_region_name'].lower() in regions: entry.print(filtered_fasta_file) |
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| diff -r dbe37a658cd2 -r 99bae410128c gstf_preparation.xml --- a/gstf_preparation.xml Sun Sep 27 18:54:31 2020 +0000 +++ b/gstf_preparation.xml Mon Oct 05 13:33:59 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="gstf_preparation" name="GeneSeqToFamily preparation" version="0.4.2"> +<tool id="gstf_preparation" name="GeneSeqToFamily preparation" version="0.4.3"> <description>converts data for the workflow</description> <requirements> <requirement type="package" version="3.7">python</requirement> @@ -47,8 +47,8 @@ <param name="headers" type="select" display="radio" label="Change the header line of the FASTA sequences to the following format" help="As required by TreeBest, part of the GeneSeqToFamily workflow, only TranscriptId_species is acceptable format by Aequatus visualisation"> <option value="TranscriptId_species" selected="true">TranscriptId_species</option> - <option value="GeneSymbol-TranscriptID_species">GeneSymbol-TranscriptID_species</option> - <option value="TranscriptSymbol-TranscriptID_species">TranscriptSymbol-TranscriptID_species</option> + <option value="TranscriptID-GeneSymbol_species">GeneSymbol-TranscriptID_species</option> + <option value="TranscriptID-TranscriptSymbol_species">TranscriptSymbol-TranscriptID_species</option> <option value="">Don't change</option> </param> <param name="regions" type="text" optional="true" label="Comma-separated list of region IDs (e.g. chromosomes or scaffolds) for which FASTA sequences should be filtered out" help="Region IDs are in the `seqid` column for GFF3 and in the `seq_region_name` field in JSON. This is typically used to filter out chromosomes with a non-standard genetic code, like mitochondria, to be analysed separately" /> |