Mercurial > repos > iuc > snpeff

changeset 24:cfcf33df7fc0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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(-) [+]
line wrap: on
line diff
--- 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