| Previous changeset 5:817031b8486d (2018-05-10) Next changeset 7:6a5282f71f82 (2018-10-11) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 133bb57feca9672734d664e6b34e428488cf2e73 |
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modified:
ete_genetree_splitter.xml ete_homology_classifier.py ete_lineage_generator.py ete_lineage_generator.xml ete_macros.xml ete_species_tree_generator.xml test-data/lineage-compress-lower.txt test-data/lineage-compress.txt test-data/lineage-full.txt test-data/lineage.txt |
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added:
test-data/lineage-wid.txt |
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| diff -r 817031b8486d -r f1eca1158f21 ete_genetree_splitter.xml --- a/ete_genetree_splitter.xml Thu May 10 06:15:17 2018 -0400 +++ b/ete_genetree_splitter.xml Wed Oct 10 05:24:04 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@.1"> +<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> |
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| diff -r 817031b8486d -r f1eca1158f21 ete_homology_classifier.py --- a/ete_homology_classifier.py Thu May 10 06:15:17 2018 -0400 +++ b/ete_homology_classifier.py Wed Oct 10 05:24:04 2018 -0400 |
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| @@ -17,8 +17,13 @@ if options.genetree is None: parser.error("--genetree option must be specified, GeneTree in nhx format") + with open(options.genetree, 'r') as f: + contents = f.read() + + # Remove empty NHX features that can be produced by TreeBest but break ete3 + contents = contents.replace('[&&NHX]', '') # reads single gene tree - genetree = PhyloTree(options.genetree) + genetree = PhyloTree(contents) leaves_list = genetree.get_leaf_names() # Genetree nodes are required to be in gene_species format |
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| diff -r 817031b8486d -r f1eca1158f21 ete_lineage_generator.py --- a/ete_lineage_generator.py Thu May 10 06:15:17 2018 -0400 +++ b/ete_lineage_generator.py Wed Oct 10 05:24:04 2018 -0400 |
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| @@ -69,6 +69,8 @@ help='Prefer lower levels when compressed') parser.add_option('-r', '--rank', dest='ranks', action="append", help='include rank - multiple ones can be specified') +parser.add_option('-i', '--includeid', dest="addid", action="store_true", default=False, + help='add taxid column') options, args = parser.parse_args() # check command line options @@ -106,8 +108,13 @@ for ilr in range(len(LONG_RANKS)): if RANKS[ir] in LONG_RANKS[ilr]: COMP_RANK_IDX[LONG_RANKS[ilr]] = ir + # write header -of.write("#species/taxid\t%s\n" % ("\t".join(RANKS))) +of.write("# query") +if options.addid: + of.write("\ttaxid") +of.write("\t%s\n" % ("\t".join(RANKS))) + # get and write data with open(options.input_species_filename) as f: for line in f.readlines(): @@ -128,5 +135,8 @@ process_taxid(ncbi, taxid, ranks, RANK_IDX) if options.compress: process_taxid(ncbi, taxid, ranks, COMP_RANK_IDX, options.lower) - of.write("%s\t%s\n" % (line, "\t".join(ranks))) + of.write("%s" % line) + if options.addid: + of.write("\t%d" % taxid) + of.write("\t%s\n" % "\t".join(ranks)) of.close() |
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| diff -r 817031b8486d -r f1eca1158f21 ete_lineage_generator.xml --- a/ete_lineage_generator.xml Thu May 10 06:15:17 2018 -0400 +++ b/ete_lineage_generator.xml Wed Oct 10 05:24:04 2018 -0400 |
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| @@ -20,6 +20,7 @@ $compresscond.compress $compresscond.lower #end if +$includeid ]]></command> <inputs> <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species/taxid per line" /> @@ -68,17 +69,16 @@ </conditional> <conditional name="compresscond"> <param name="compress" type="select" label="Fill unnamed ranks" help="Fill unnamed ranks with super/sub ranks (see -l)"> - <option value="-c">Yes</option> + <option value="-c" selected="True">Yes</option> <option value="">No</option> </param> <when value="-c"> - <param name="lower" type="select" label="Prefer lower ranks for filling" help="Prefer lower levels for filling"> - <option value="-l">Yes</option> - <option value="">No</option> - </param> + <param name="lower" type="boolean" truevalue="-l" falsevalue="" checked="False" label="Prefer lower ranks" help="Take the next available lower rank (default: higher)"/> </when> <when value="" /> </conditional> + <param name="includeid" type="boolean" truevalue="--includeid" falsevalue="" label="Include taxid in the table" + help="For the case when the input consists of taxon names" /> </inputs> <outputs> <data name="outputFile" format="tsv" label="${tool.name} on ${on_string}"/> @@ -114,6 +114,12 @@ <param name="manualranks" value="kingdom,family" /> <output name="outputFile" file="lineage-full.txt" /> </test> + <test> + <param name="speciesFile" ftype="txt" value="species.txt" /> + <param name="database" ftype="sqlite" value="taxdump.sqlite" /> + <param name="includeid" value="--includeid" /> + <output name="outputFile" file="lineage-wid.txt" /> + </test> </tests> <help><![CDATA[ Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the `ETE Toolkit`_. |
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| diff -r 817031b8486d -r f1eca1158f21 ete_macros.xml --- a/ete_macros.xml Thu May 10 06:15:17 2018 -0400 +++ b/ete_macros.xml Wed Oct 10 05:24:04 2018 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">3.0.0b35</token> + <token name="@VERSION@">3.1.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">ete3</requirement> |
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| diff -r 817031b8486d -r f1eca1158f21 ete_species_tree_generator.xml --- a/ete_species_tree_generator.xml Thu May 10 06:15:17 2018 -0400 +++ b/ete_species_tree_generator.xml Wed Oct 10 05:24:04 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ete_species_tree_generator" name="ETE species tree generator" version="@VERSION@.1"> +<tool id="ete_species_tree_generator" name="ETE species tree generator" version="@VERSION@"> <description>from a list of species using the ETE Toolkit</description> <macros> <import>ete_macros.xml</import> |
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| diff -r 817031b8486d -r f1eca1158f21 test-data/lineage-compress-lower.txt --- a/test-data/lineage-compress-lower.txt Thu May 10 06:15:17 2018 -0400 +++ b/test-data/lineage-compress-lower.txt Wed Oct 10 05:24:04 2018 -0400 |
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| @@ -1,4 +1,4 @@ -#species/taxid kingdom phylum class order family genus species +# query kingdom phylum class order family genus species Latimeria chalumnae Eukaryota Chordata NA Coelacanthiformes Coelacanthidae Latimeria Latimeria chalumnae Xenopus tropicalis Eukaryota Chordata Amphibia Batrachia Pipoidea Xenopus Xenopus tropicalis Ornithorhynchus anatinus Eukaryota Chordata Mammalia Monotremata Ornithorhynchidae Ornithorhynchus Ornithorhynchus anatinus |
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| diff -r 817031b8486d -r f1eca1158f21 test-data/lineage-compress.txt --- a/test-data/lineage-compress.txt Thu May 10 06:15:17 2018 -0400 +++ b/test-data/lineage-compress.txt Wed Oct 10 05:24:04 2018 -0400 |
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| @@ -1,4 +1,4 @@ -#species/taxid kingdom phylum class order family genus species +# query kingdom phylum class order family genus species Latimeria chalumnae Eukaryota Chordata NA Coelacanthiformes Coelacanthidae Latimeria Latimeria chalumnae Xenopus tropicalis Eukaryota Chordata Amphibia Batrachia Pipoidea Xenopus Xenopus tropicalis Ornithorhynchus anatinus Eukaryota Chordata Mammalia Monotremata Ornithorhynchidae Ornithorhynchus Ornithorhynchus anatinus |
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| diff -r 817031b8486d -r f1eca1158f21 test-data/lineage-full.txt --- a/test-data/lineage-full.txt Thu May 10 06:15:17 2018 -0400 +++ b/test-data/lineage-full.txt Wed Oct 10 05:24:04 2018 -0400 |
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| @@ -1,4 +1,4 @@ -#species/taxid kingdom family +# query kingdom family Latimeria chalumnae Metazoa Coelacanthidae Xenopus tropicalis Metazoa Pipidae Ornithorhynchus anatinus Metazoa Ornithorhynchidae |
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| diff -r 817031b8486d -r f1eca1158f21 test-data/lineage-wid.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineage-wid.txt Wed Oct 10 05:24:04 2018 -0400 |
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| @@ -0,0 +1,63 @@ +# query taxid kingdom phylum class order family genus species +Latimeria chalumnae 7897 Eukaryota Chordata NA Coelacanthiformes Coelacanthidae Latimeria Latimeria chalumnae +Xenopus tropicalis 8364 Eukaryota Chordata Amphibia Batrachia Pipoidea Xenopus Xenopus tropicalis +Ornithorhynchus anatinus 9258 Eukaryota Chordata Mammalia Monotremata Ornithorhynchidae Ornithorhynchus Ornithorhynchus anatinus +Macropus eugenii 9315 Eukaryota Chordata Mammalia Diprotodontia Macropodidae Notamacropus Notamacropus eugenii +Sarcophilus harrisii 9305 Eukaryota Chordata Mammalia Dasyuromorphia Dasyuridae Sarcophilus Sarcophilus harrisii +Monodelphis domestica 13616 Eukaryota Chordata Mammalia Didelphimorphia Didelphidae Monodelphis Monodelphis domestica +Echinops telfairi 9371 Eukaryota Chordata Mammalia Afrotheria Tenrecidae Echinops Echinops telfairi +Procavia capensis 9813 Eukaryota Chordata Mammalia Afrotheria Procaviidae Procavia Procavia capensis +Loxodonta africana 9785 Eukaryota Chordata Mammalia Afrotheria Elephantidae Loxodonta Loxodonta africana +Dasypus novemcinctus 9361 Eukaryota Chordata Mammalia Xenarthra Dasypodidae Dasypus Dasypus novemcinctus +Choloepus hoffmanni 9358 Eukaryota Chordata Mammalia Xenarthra Megalonychidae Choloepus Choloepus hoffmanni +Ochotona princeps 9978 Eukaryota Chordata Mammalia Euarchontoglires Ochotonidae Ochotona Ochotona princeps +Oryctolagus cuniculus 9986 Eukaryota Chordata Mammalia Euarchontoglires Leporidae Oryctolagus Oryctolagus cuniculus +Cavia porcellus 10141 Eukaryota Chordata Mammalia Euarchontoglires Caviidae Cavia Cavia porcellus +Ictidomys tridecemlineatus 43179 Eukaryota Chordata Mammalia Euarchontoglires Sciuridae Ictidomys Ictidomys tridecemlineatus +Dipodomys ordii 10020 Eukaryota Chordata Mammalia Euarchontoglires Heteromyidae Dipodomys Dipodomys ordii +Rattus norvegicus 10116 Eukaryota Chordata Mammalia Euarchontoglires Muridae Rattus Rattus norvegicus +Mus musculus 10090 Eukaryota Chordata Mammalia Euarchontoglires Muridae Mus Mus musculus +Tupaia belangeri 37347 Eukaryota Chordata Mammalia Euarchontoglires Tupaiidae Tupaia Tupaia belangeri +Otolemur garnettii 30611 Eukaryota Chordata Mammalia Euarchontoglires Galagidae Otolemur Otolemur garnettii +Microcebus murinus 30608 Eukaryota Chordata Mammalia Euarchontoglires Cheirogaleidae Microcebus Microcebus murinus +Tarsius syrichta 1868482 Eukaryota Chordata Mammalia Euarchontoglires Tarsiidae Carlito Carlito syrichta +Callithrix jacchus 9483 Eukaryota Chordata Mammalia Euarchontoglires Cebidae Callithrix Callithrix jacchus +Chlorocebus sabaeus 60711 Eukaryota Chordata Mammalia Euarchontoglires Cercopithecoidea Chlorocebus Chlorocebus sabaeus +Papio anubis 9555 Eukaryota Chordata Mammalia Euarchontoglires Cercopithecoidea Papio Papio anubis +Macaca mulatta 9544 Eukaryota Chordata Mammalia Euarchontoglires Cercopithecoidea Macaca Macaca mulatta +Nomascus leucogenys 61853 Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Nomascus Nomascus leucogenys +Pongo abelii 9601 Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Pongo Pongo abelii +Gorilla gorilla gorilla 9595 Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Gorilla Gorilla gorilla +Pan troglodytes 9598 Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Pan Pan troglodytes +Homo sapiens 9606 Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Homo Homo sapiens +Sorex araneus 42254 Eukaryota Chordata Mammalia Laurasiatheria Soricidae Sorex Sorex araneus +Erinaceus europaeus 9365 Eukaryota Chordata Mammalia Laurasiatheria Erinaceidae Erinaceus Erinaceus europaeus +Pteropus vampyrus 132908 Eukaryota Chordata Mammalia Laurasiatheria Pteropodidae Pteropus Pteropus vampyrus +Myotis lucifugus 59463 Eukaryota Chordata Mammalia Laurasiatheria Vespertilionidae Myotis Myotis lucifugus +Felis catus 9685 Eukaryota Chordata Mammalia Laurasiatheria Felidae Felis Felis catus +Canis lupus familiaris 9615 Eukaryota Chordata Mammalia Laurasiatheria Canidae Canis Canis lupus +Mustela putorius furo 9669 Eukaryota Chordata Mammalia Laurasiatheria Mustelidae Mustela Mustela putorius +Ailuropoda melanoleuca 9646 Eukaryota Chordata Mammalia Laurasiatheria Ursidae Ailuropoda Ailuropoda melanoleuca +Equus caballus 9796 Eukaryota Chordata Mammalia Laurasiatheria Equidae Equus Equus caballus +Vicugna pacos 30538 Eukaryota Chordata Mammalia Laurasiatheria Camelidae Vicugna Vicugna pacos +Sus scrofa 9823 Eukaryota Chordata Mammalia Laurasiatheria Suidae Sus Sus scrofa +Tursiops truncatus 9739 Eukaryota Chordata Mammalia Laurasiatheria Delphinidae Tursiops Tursiops truncatus +Ovis aries 9940 Eukaryota Chordata Mammalia Laurasiatheria Bovidae Ovis Ovis aries +Bos taurus 9913 Eukaryota Chordata Mammalia Laurasiatheria Bovidae Bos Bos taurus +Anolis carolinensis 28377 Eukaryota Chordata NA Lepidosauria Dactyloidae Anolis Anolis carolinensis +Pelodiscus sinensis 13735 Eukaryota Chordata NA Testudines Trionychidae Pelodiscus Pelodiscus sinensis +Taeniopygia guttata 59729 Eukaryota Chordata Aves Neognathae Passeroidea Taeniopygia Taeniopygia guttata +Ficedula albicollis 59894 Eukaryota Chordata Aves Neognathae Muscicapidae Ficedula Ficedula albicollis +Anas platyrhynchos 8839 Eukaryota Chordata Aves Neognathae Anatidae Anas Anas platyrhynchos +Meleagris gallopavo 9103 Eukaryota Chordata Aves Neognathae Phasianidae Meleagris Meleagris gallopavo +Gallus gallus 9031 Eukaryota Chordata Aves Neognathae Phasianidae Gallus Gallus gallus +Lepisosteus oculatus 7918 Eukaryota Chordata Actinopterygii Semionotiformes Lepisosteidae Lepisosteus Lepisosteus oculatus +Danio rerio 7955 Eukaryota Chordata Actinopterygii Cypriniphysae Cyprinoidea Danio Danio rerio +Astyanax mexicanus 7994 Eukaryota Chordata Actinopterygii Characiphysae Characidae Astyanax Astyanax mexicanus +Gadus morhua 8049 Eukaryota Chordata Actinopterygii Gadiformes Gadidae Gadus Gadus morhua +Oreochromis niloticus 8128 Eukaryota Chordata Actinopterygii Cichlomorphae Cichlidae Oreochromis Oreochromis niloticus +Poecilia formosa 48698 Eukaryota Chordata Actinopterygii Atherinomorphae Poeciliidae Poecilia Poecilia formosa +Xiphophorus maculatus 8083 Eukaryota Chordata Actinopterygii Atherinomorphae Poeciliidae Xiphophorus Xiphophorus maculatus +Gasterosteus aculeatus 69293 Eukaryota Chordata Actinopterygii Perciformes Gasterosteidae Gasterosteus Gasterosteus aculeatus +Tetraodon nigroviridis 99883 Eukaryota Chordata Actinopterygii Tetraodontiformes Tetradontoidea Tetraodon Tetraodon nigroviridis +Takifugu rubripes 31033 Eukaryota Chordata Actinopterygii Tetraodontiformes Tetradontoidea Takifugu Takifugu rubripes |
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| diff -r 817031b8486d -r f1eca1158f21 test-data/lineage.txt --- a/test-data/lineage.txt Thu May 10 06:15:17 2018 -0400 +++ b/test-data/lineage.txt Wed Oct 10 05:24:04 2018 -0400 |
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| @@ -1,4 +1,4 @@ -#species/taxid superkingdom kingdom subkingdom superphylum phylum subphylum superclass class subclass infraclass cohort superorder order suborder infraorder parvorder superfamily family subfamily tribe subtribe genus subgenus species group species subgroup species subspecies varietas forma +# query superkingdom kingdom subkingdom superphylum phylum subphylum superclass class subclass infraclass cohort superorder order suborder infraorder parvorder superfamily family subfamily tribe subtribe genus subgenus species group species subgroup species subspecies varietas forma Latimeria chalumnae Eukaryota Metazoa NA NA Chordata Craniata NA NA NA NA NA NA Coelacanthiformes NA NA NA NA Coelacanthidae NA NA NA Latimeria NA NA NA Latimeria chalumnae NA NA NA Xenopus tropicalis Eukaryota Metazoa NA NA Chordata Craniata NA Amphibia NA NA NA Batrachia Anura NA NA NA Pipoidea Pipidae Xenopodinae NA NA Xenopus Silurana NA NA Xenopus tropicalis NA NA NA Ornithorhynchus anatinus Eukaryota Metazoa NA NA Chordata Craniata NA Mammalia NA NA NA NA Monotremata NA NA NA NA Ornithorhynchidae NA NA NA Ornithorhynchus NA NA NA Ornithorhynchus anatinus NA NA NA |