Mercurial > repos > earlhaminst > ete
changeset 15:1e85af7a29c4 draft default tip
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
| author | earlhaminst |
|---|---|
| date | Mon, 24 Feb 2025 16:34:12 +0000 |
| parents | d40b9a7debe5 |
| children | |
| files | ete_gene_cnv.xml ete_genetree_splitter.xml ete_homology_classifier.xml ete_init_taxdb.py ete_init_taxdb.xml ete_lineage_generator.xml ete_macros.xml ete_mod.xml ete_species_tree_generator.py ete_species_tree_generator.xml |
| diffstat | 10 files changed, 33 insertions(+), 24 deletions(-) [+] |
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--- 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>
--- 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:**
--- 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:**
--- 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)
--- 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**
--- 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**
--- 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>
--- 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>
--- 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]
--- 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:**