fixes for tests to pass, switch to bioperl 1.7.2

EngyNasr · May 21, 2020 · 56a5799 · 56a5799
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commit 56a5799
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Showing 4 changed files with 4 additions and 5 deletions.
diff --git a/tools/bioperl/bp_genbank2gff3.xml b/tools/bioperl/bp_genbank2gff3.xml
@@ -1,4 +1,4 @@
-<tool id="bp_genbank2gff3" name="Genbank to GFF3" version="1.0">
+<tool id="bp_genbank2gff3" name="Genbank to GFF3" version="1.0a">
   <description>converter</description>
   <macros>
       <import>macros.xml</import>

diff --git a/tools/bioperl/macros.xml b/tools/bioperl/macros.xml
@@ -1,8 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.6.924">perl-bioperl</requirement>
-            <requirement type="package" version="1.007002">perl-bioperl-core</requirements>
+            <requirement type="package" version="1.7.2">perl-bioperl</requirement>
             <yield/>
         </requirements>
     </xml>

diff --git a/tools/bioperl/test-data/seq.gb.0.gff b/tools/bioperl/test-data/seq.gb.0.gff
@@ -6,7 +6,7 @@
 # Note Enterobacteria phage CC31, complete genome.
 # date 12-NOV-2010
 # working on contig:NC_014662, Enterobacteria phage CC31, Enterobacteria phage CC31, complete genome., 12-NOV-2010
-NC_014662	GenBank	contig	1	165540	.	+	1	ID=NC_014662;Dbxref=BioProject:PRJNA60119,taxon:709484;Name=NC_014662;Note=Enterobacteria phage CC31%2C complete genome.,PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318. COMPLETENESS: full length. ;comment1=PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318. COMPLETENESS: full length. ;date=12-NOV-2010;host=Escherichia coli;mol_type=genomic DNA;organism=Enterobacteria phage CC31
+NC_014662	GenBank	contig	1	165540	.	+	1	ID=NC_014662;Dbxref=BioProject:PRJNA60119,taxon:709484;Name=NC_014662;Note=Enterobacteria phage CC31%2C complete genome.,PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318.  COMPLETENESS: full length. ;comment1=PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318.  COMPLETENESS: full length. ;date=12-NOV-2010;host=Escherichia coli;mol_type=genomic DNA;organism=Enterobacteria phage CC31
 NC_014662	GenBank	gene	1	2214	.	-	1	ID=CC31p001;Dbxref=GeneID:9926434;Name=rIIA;locus_tag=CC31p001
 NC_014662	GenBank	mRNA	1	2214	.	-	1	ID=CC31p001.t01;Parent=CC31p001
 NC_014662	GenBank	CDS	1	2214	.	-	1	ID=CC31p001.p01;Parent=CC31p001.t01;Dbxref=GI:311992993,GeneID:9926434;Name=rIIA;codon_start=1;locus_tag=CC31p001;product=membrane-associated affects host membrane ATPase;protein_id=YP_004009859.1;transl_table=11;translation=length.737

diff --git a/tools/bioperl/test-data/seq.gb.1.gff b/tools/bioperl/test-data/seq.gb.1.gff
@@ -6,7 +6,7 @@
 # Note Enterobacteria phage CC31, complete genome.
 # date 12-NOV-2010
 # working on contig:NC_014662, Enterobacteria phage CC31, Enterobacteria phage CC31, complete genome., 12-NOV-2010
-NC_014662	GenBank	contig	1	165540	.	+	1	ID=NC_014662;Dbxref=BioProject:PRJNA60119,taxon:709484;Name=NC_014662;Note=Enterobacteria phage CC31%2C complete genome.,PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318. COMPLETENESS: full length. ;comment1=PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318. COMPLETENESS: full length. ;date=12-NOV-2010;host=Escherichia coli;mol_type=genomic DNA;organism=Enterobacteria phage CC31
+NC_014662	GenBank	contig	1	165540	.	+	1	ID=NC_014662;Dbxref=BioProject:PRJNA60119,taxon:709484;Name=NC_014662;Note=Enterobacteria phage CC31%2C complete genome.,PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318.  COMPLETENESS: full length. ;comment1=PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to GU323318.  COMPLETENESS: full length. ;date=12-NOV-2010;host=Escherichia coli;mol_type=genomic DNA;organism=Enterobacteria phage CC31
 NC_014662	GenBank	gene	1	2214	.	-	1	ID=CC31p001;Dbxref=GeneID:9926434;Name=rIIA;locus_tag=CC31p001
 NC_014662	GenBank	mRNA	1	2214	.	-	1	ID=CC31p001.t01;Parent=CC31p001
 NC_014662	GenBank	CDS	1	2214	.	-	1	ID=CC31p001.p01;Parent=CC31p001.t01;Dbxref=GI:311992993,GeneID:9926434;Name=rIIA;codon_start=1;locus_tag=CC31p001;product=membrane-associated affects host membrane ATPase;protein_id=YP_004009859.1;transl_table=11;translation=length.737