Mercurial > repos > iuc > snpeff
changeset 24:cfcf33df7fc0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4366b6a23223f84039a0590cf0d7079b83d8f84"
| author | iuc |
|---|---|
| date | Wed, 13 Oct 2021 23:30:29 +0000 |
| parents | 74aebe30fb52 |
| children | 5c7b70713fb5 |
| files | gbk2fa.py snpEff_create_db.xml snpEff_macros.xml test-data/pBR322.gff3 |
| diffstat | 4 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/gbk2fa.py Sun Jan 19 09:43:43 2020 -0500 +++ b/gbk2fa.py Wed Oct 13 23:30:29 2021 +0000 @@ -39,5 +39,5 @@ seq_id = seq_record.id.split('.')[0] else: seq_id = seq_record.id - print('Writing FASTA record: {}'.format( seq_id )) + print('Writing FASTA record: {}'.format(seq_id)) output_handle.write(">{}\n{}\n".format(seq_id, seq_record.seq))
--- a/snpEff_create_db.xml Sun Jan 19 09:43:43 2020 -0500 +++ b/snpEff_create_db.xml Wed Oct 13 23:30:29 2021 +0000 @@ -186,7 +186,7 @@ <param name="input_type_selector" value="gff"/> <param name="reference_source_selector" value="history"/> <param name="input_fasta" value="pBR322_test2.fna" /> - <param name="input_gff" value="pBR322.gff3" /> + <param name="input_gff" value="pBR322.gff3"/> <output name="snpeff_output"> <assert_contents> <has_text text="pBR322" /> @@ -198,7 +198,7 @@ <param name="input_type_selector" value="gff"/> <param name="reference_source_selector" value="history"/> <param name="input_fasta" value="pBR322_test2.fna.gz" /> - <param name="input_gff" value="pBR322.gff3" /> + <param name="input_gff" value="pBR322.gff3"/> <output name="snpeff_output"> <assert_contents> <has_text text="pBR322" />
--- a/snpEff_macros.xml Sun Jan 19 09:43:43 2020 -0500 +++ b/snpEff_macros.xml Wed Oct 13 23:30:29 2021 +0000 @@ -37,7 +37,7 @@ **Pre-cached databases** -Many standard (e.g., human, mouse, *Drosophila*) databases are likely pre-cached within a given Galaxy instance. You should be able to see them listed in **Genome** drop-down of **SbpEff eff** tool. +Many standard (e.g., human, mouse, *Drosophila*) databases are likely pre-cached within a given Galaxy instance. You should be able to see them listed in **Genome** drop-down of **SnpEff eff** tool. In you *do not see them* keep reading...
--- a/test-data/pBR322.gff3 Sun Jan 19 09:43:43 2020 -0500 +++ b/test-data/pBR322.gff3 Wed Oct 13 23:30:29 2021 +0000 @@ -1,3 +1,4 @@ +##gff-version 3 ##sequence-region J01749.1 1 4361 ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=47470 J01749.1 Genbank region 1 4361 . + . ID=id-1;Dbxref=taxon:47470;Is_circular=true;gbkey=Src;mol_type=other DNA;tissue-lib=ATCC 31344%2C ATCC 37017