# HG changeset patch
# User earlhaminst
# Date 1740414852 0
# Node ID 1e85af7a29c48903532fb016098482c49e589773
# Parent  d40b9a7debe5c60f30c81f0955d7402b98e6fd50
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty

diff -r d40b9a7debe5 -r 1e85af7a29c4 ete_gene_cnv.xml
--- a/ete_gene_cnv.xml	Thu Mar 07 19:39:30 2024 +0000
+++ b/ete_gene_cnv.xml	Mon Feb 24 16:34:12 2025 +0000
@@ -28,7 +28,7 @@
     <help><![CDATA[
 Find copy number for genes from GeneTree by utilising the `ETE Toolkit`_. Input can be single GeneTree or multiple GeneTree in a file with one GeneTree per line.
 
-.. _ETE Toolkit: http://etetoolkit.org/
+.. _ETE Toolkit: https://etetoolkit.org/
     ]]></help>
     <expand macro="citations" />
 </tool>
diff -r d40b9a7debe5 -r 1e85af7a29c4 ete_genetree_splitter.xml
--- a/ete_genetree_splitter.xml	Thu Mar 07 19:39:30 2024 +0000
+++ b/ete_genetree_splitter.xml	Mon Feb 24 16:34:12 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@+galaxy1">
+<tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@">
     <description>from a genetree using the ETE Toolkit</description>
     <macros>
         <import>ete_macros.xml</import>
@@ -147,7 +147,7 @@
     <help><![CDATA[
 Split GeneTrees from single GeneTree by duplication event using the `ETE Toolkit`_.
 
-.. _ETE Toolkit: http://etetoolkit.org/
+.. _ETE Toolkit: https://etetoolkit.org/
 
 **Output format:**
 
diff -r d40b9a7debe5 -r 1e85af7a29c4 ete_homology_classifier.xml
--- a/ete_homology_classifier.xml	Thu Mar 07 19:39:30 2024 +0000
+++ b/ete_homology_classifier.xml	Mon Feb 24 16:34:12 2025 +0000
@@ -64,7 +64,7 @@
     <![CDATA[
 Classify and filter Homology from single GeneTree by utilising the `ETE Toolkit`_.
 
-.. _ETE Toolkit: http://etetoolkit.org/
+.. _ETE Toolkit: https://etetoolkit.org/
 
 **Output format:**
 
diff -r d40b9a7debe5 -r 1e85af7a29c4 ete_init_taxdb.py
--- a/ete_init_taxdb.py	Thu Mar 07 19:39:30 2024 +0000
+++ b/ete_init_taxdb.py	Mon Feb 24 16:34:12 2025 +0000
@@ -1,24 +1,32 @@
 import optparse
+from urllib.request import urlretrieve
 
-import ete3.ncbi_taxonomy
-from six.moves.urllib.request import urlretrieve
+from ete3.ncbi_taxonomy.ncbiquery import update_db
 
 parser = optparse.OptionParser()
-parser.add_option('-t', '--taxdump', dest='taxdump', default=None,
-                  help='NCBI taxdump (tar.gz) will be downloaded if not given')
-parser.add_option('-d', '--database', dest="database", default=None,
-                  help='ETE sqlite data base to use (default: ~/.etetoolkit/taxa.sqlite)')
+parser.add_option(
+    "-t",
+    "--taxdump",
+    dest="taxdump",
+    default=None,
+    help="NCBI taxdump (tar.gz), will be downloaded if not given",
+)
+parser.add_option(
+    "-d",
+    "--database",
+    dest="database",
+    default=None,
+    help="ETE sqlite data base to create",
+)
 options, args = parser.parse_args()
 if options.database is None:
     parser.error("-d option must be specified")
 if options.taxdump is not None:
     taxdump = options.taxdump
 else:
-    urlretrieve("http://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", "taxdump.tar.gz")
+    urlretrieve(
+        "https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", "taxdump.tar.gz"
+    )
     taxdump = "taxdump.tar.gz"
 
-# will remove a taxdump.tar.gz file at the end
-# which will lead to an errmessage if not present
-# if the tool is run on a taxdump in the current dir it will be
-# deleted in the end
-ete3.ncbi_taxonomy.ncbiquery.update_db(dbfile=options.database, targz_file=taxdump)
+update_db(dbfile=options.database, targz_file=taxdump)
diff -r d40b9a7debe5 -r 1e85af7a29c4 ete_init_taxdb.xml
--- a/ete_init_taxdb.xml	Thu Mar 07 19:39:30 2024 +0000
+++ b/ete_init_taxdb.xml	Mon Feb 24 16:34:12 2025 +0000
@@ -37,7 +37,7 @@
     <help><![CDATA[
 Generates the ETE sqlite data base from the NCBI taxdump.tar.gz using the `ETE Toolkit`_.
 
-.. _ETE Toolkit: http://etetoolkit.org/
+.. _ETE Toolkit: https://etetoolkit.org/
 
 **Input**
 
diff -r d40b9a7debe5 -r 1e85af7a29c4 ete_lineage_generator.xml
--- a/ete_lineage_generator.xml	Thu Mar 07 19:39:30 2024 +0000
+++ b/ete_lineage_generator.xml	Mon Feb 24 16:34:12 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="ete_lineage_generator" name="ETE lineage generator" version="@VERSION@+galaxy1">
+<tool id="ete_lineage_generator" name="ETE lineage generator" version="@VERSION@">
     <description>from a list of species/taxids using the ETE Toolkit</description>
     <macros>
         <import>ete_macros.xml</import>
@@ -138,7 +138,7 @@
     <help><![CDATA[
 Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the `ETE Toolkit`_.
 
-.. _ETE Toolkit: http://etetoolkit.org/
+.. _ETE Toolkit: https://etetoolkit.org/
 
 **Input**
 
diff -r d40b9a7debe5 -r 1e85af7a29c4 ete_macros.xml
--- a/ete_macros.xml	Thu Mar 07 19:39:30 2024 +0000
+++ b/ete_macros.xml	Mon Feb 24 16:34:12 2025 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">3.1.2</token>
+    <token name="@VERSION@">3.1.3</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">ete</xref>
diff -r d40b9a7debe5 -r 1e85af7a29c4 ete_mod.xml
--- a/ete_mod.xml	Thu Mar 07 19:39:30 2024 +0000
+++ b/ete_mod.xml	Mon Feb 24 16:34:12 2025 +0000
@@ -105,7 +105,7 @@
     <help><![CDATA[
 Modify a given input tree using the `ETE Toolkit`_.
 
-.. _ETE Toolkit: http://etetoolkit.org/
+.. _ETE Toolkit: https://etetoolkit.org/
     ]]></help>
     <expand macro="citations" />
 </tool>
diff -r d40b9a7debe5 -r 1e85af7a29c4 ete_species_tree_generator.py
--- a/ete_species_tree_generator.py	Thu Mar 07 19:39:30 2024 +0000
+++ b/ete_species_tree_generator.py	Mon Feb 24 16:34:12 2025 +0000
@@ -18,10 +18,11 @@
 if options.input_species_filename is None:
     parser.error("-s option must be specified, Species list in text format one species in each line")
 
-ncbi = NCBITaxa(dbfile=options.database)
+ncbi = NCBITaxa(dbfile=options.database, update=False)
 with open(options.input_species_filename) as f:
     species_name = [_.strip().replace('_', ' ') for _ in f.readlines()]
 
+breakpoint()
 name2taxid = ncbi.get_name_translator(species_name)
 
 taxid = [name2taxid[_][0] for _ in species_name]
diff -r d40b9a7debe5 -r 1e85af7a29c4 ete_species_tree_generator.xml
--- a/ete_species_tree_generator.xml	Thu Mar 07 19:39:30 2024 +0000
+++ b/ete_species_tree_generator.xml	Mon Feb 24 16:34:12 2025 +0000
@@ -23,7 +23,7 @@
     ]]></command>
     <inputs>
         <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" />
-        <param name="database" type="data" format="sqlite" label="(ETE3) Taxonomy Database" help="The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)" />
+        <param name="database" type="data" format="sqlite" label="ETE3 Taxonomy Database" help="The SQLite Taxonomy Database generated by the 'ETE taxa DB generator' tool" />
         <conditional name="output_format">
             <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest">
                 <option value="yes">Yes</option>
@@ -66,7 +66,7 @@
     <help><![CDATA[
 Generate a species tree from a list of species using the `ETE Toolkit`_.
 
-.. _ETE Toolkit: http://etetoolkit.org/
+.. _ETE Toolkit: https://etetoolkit.org/
 
 **Output format:**