Mercurial > repos > galaxyp > translate_bed
diff macros.xml @ 0:038ecf54cbec draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed commit 383bb485120a193bcc14f88364e51356d6ede219
| author | galaxyp |
|---|---|
| date | Mon, 22 Jan 2018 13:59:27 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jan 22 13:59:27 2018 -0500 @@ -0,0 +1,125 @@ +<macros> + <xml name="bedutil_requirements"> + <requirement type="package" version="1.62">biopython</requirement> + </xml> + <xml name="ensembl_requirements"> + <requirement type="package" version="0.4.10">requests-cache</requirement> + </xml> + <xml name="twobit_requirements"> + <requirement type="package" version="3.1.4">twobitreader</requirement> + </xml> + <xml name="species_options"> + <option value="homo_sapiens">homo_sapiens (Human) taxon_id: 9606</option> + <option value="mus_musculus">mus_musculus (Mouse) taxon_id: 10090</option> + <option value="ailuropoda_melanoleuca">ailuropoda_melanoleuca (Panda) taxon_id: 9646</option> + <option value="anas_platyrhynchos">anas_platyrhynchos (Duck) taxon_id: 8839</option> + <option value="anolis_carolinensis">anolis_carolinensis (Anole lizard) taxon_id: 28377</option> + <option value="astyanax_mexicanus">astyanax_mexicanus (Cave fish) taxon_id: 7994</option> + <option value="bos_taurus">bos_taurus (Cow) taxon_id: 9913</option> + <option value="caenorhabditis_elegans">caenorhabditis_elegans (Caenorhabditis elegans) taxon_id: 6239</option> + <option value="callithrix_jacchus">callithrix_jacchus (Marmoset) taxon_id: 9483</option> + <option value="canis_familiaris">canis_familiaris (Dog) taxon_id: 9615</option> + <option value="carlito_syrichta">carlito_syrichta (Tarsier) taxon_id: 1868482</option> + <option value="cavia_aperea">cavia_aperea (Brazilian guinea pig) taxon_id: 37548</option> + <option value="cavia_porcellus">cavia_porcellus (Guinea Pig) taxon_id: 10141</option> + <option value="chinchilla_lanigera">chinchilla_lanigera (Long-tailed chinchilla) taxon_id: 34839</option> + <option value="chlorocebus_sabaeus">chlorocebus_sabaeus (Vervet-AGM) taxon_id: 60711</option> + <option value="choloepus_hoffmanni">choloepus_hoffmanni (Sloth) taxon_id: 9358</option> + <option value="ciona_intestinalis">ciona_intestinalis (C.intestinalis) taxon_id: 7719</option> + <option value="ciona_savignyi">ciona_savignyi (C.savignyi) taxon_id: 51511</option> + <option value="cricetulus_griseus_chok1gshd">cricetulus_griseus_chok1gshd (Chinese hamster CHOK1GS) taxon_id: 10029</option> + <option value="cricetulus_griseus_crigri">cricetulus_griseus_crigri (Chinese hamster CriGri) taxon_id: 10029</option> + <option value="danio_rerio">danio_rerio (Zebrafish) taxon_id: 7955</option> + <option value="dasypus_novemcinctus">dasypus_novemcinctus (Armadillo) taxon_id: 9361</option> + <option value="dipodomys_ordii">dipodomys_ordii (Kangaroo rat) taxon_id: 10020</option> + <option value="drosophila_melanogaster">drosophila_melanogaster (Fruitfly) taxon_id: 7227</option> + <option value="echinops_telfairi">echinops_telfairi (Lesser hedgehog tenrec) taxon_id: 9371</option> + <option value="equus_caballus">equus_caballus (Horse) taxon_id: 9796</option> + <option value="erinaceus_europaeus">erinaceus_europaeus (Hedgehog) taxon_id: 9365</option> + <option value="felis_catus">felis_catus (Cat) taxon_id: 9685</option> + <option value="ficedula_albicollis">ficedula_albicollis (Flycatcher) taxon_id: 59894</option> + <option value="fukomys_damarensis">fukomys_damarensis (Damara mole rat) taxon_id: 885580</option> + <option value="gadus_morhua">gadus_morhua (Cod) taxon_id: 8049</option> + <option value="gallus_gallus">gallus_gallus (Chicken) taxon_id: 9031</option> + <option value="gasterosteus_aculeatus">gasterosteus_aculeatus (Stickleback) taxon_id: 69293</option> + <option value="gorilla_gorilla">gorilla_gorilla (Gorilla) taxon_id: 9595</option> + <option value="heterocephalus_glaber_female">heterocephalus_glaber_female (Naked mole-rat female) taxon_id: 10181</option> + <option value="heterocephalus_glaber_male">heterocephalus_glaber_male (Naked mole-rat male) taxon_id: 10181</option> + <option value="ictidomys_tridecemlineatus">ictidomys_tridecemlineatus (Squirrel) taxon_id: 43179</option> + <option value="jaculus_jaculus">jaculus_jaculus (Lesser Egyptian jerboa) taxon_id: 51337</option> + <option value="latimeria_chalumnae">latimeria_chalumnae (Coelacanth) taxon_id: 7897</option> + <option value="lepisosteus_oculatus">lepisosteus_oculatus (Spotted gar) taxon_id: 7918</option> + <option value="loxodonta_africana">loxodonta_africana (Elephant) taxon_id: 9785</option> + <option value="macaca_mulatta">macaca_mulatta (Macaque) taxon_id: 9544</option> + <option value="meleagris_gallopavo">meleagris_gallopavo (Turkey) taxon_id: 9103</option> + <option value="mesocricetus_auratus">mesocricetus_auratus (Golden Hamster) taxon_id: 10036</option> + <option value="microcebus_murinus">microcebus_murinus (Mouse Lemur) taxon_id: 30608</option> + <option value="microtus_ochrogaster">microtus_ochrogaster (Prairie vole) taxon_id: 79684</option> + <option value="monodelphis_domestica">monodelphis_domestica (Opossum) taxon_id: 13616</option> + <option value="mus_caroli">mus_caroli (Ryukyu mouse) taxon_id: 10089</option> + <option value="mus_musculus_129s1svimj">mus_musculus_129s1svimj (Mouse 129S1/SvImJ) taxon_id: 10090</option> + <option value="mus_musculus_aj">mus_musculus_aj (Mouse A/J) taxon_id: 10090</option> + <option value="mus_musculus_akrj">mus_musculus_akrj (Mouse AKR/J) taxon_id: 10090</option> + <option value="mus_musculus_balbcj">mus_musculus_balbcj (Mouse BALB/cJ) taxon_id: 10090</option> + <option value="mus_musculus_c3hhej">mus_musculus_c3hhej (Mouse C3H/HeJ) taxon_id: 10090</option> + <option value="mus_musculus_c57bl6nj">mus_musculus_c57bl6nj (Mouse C57BL/6NJ) taxon_id: 10090</option> + <option value="mus_musculus_casteij">mus_musculus_casteij (Mouse CAST/EiJ) taxon_id: 10091</option> + <option value="mus_musculus_cbaj">mus_musculus_cbaj (Mouse CBA/J) taxon_id: 10090</option> + <option value="mus_musculus_dba2j">mus_musculus_dba2j (Mouse DBA/2J) taxon_id: 10090</option> + <option value="mus_musculus_fvbnj">mus_musculus_fvbnj (Mouse FVB/NJ) taxon_id: 10090</option> + <option value="mus_musculus_lpj">mus_musculus_lpj (Mouse LP/J) taxon_id: 10090</option> + <option value="mus_musculus_nodshiltj">mus_musculus_nodshiltj (Mouse NOD/ShiLtJ) taxon_id: 10090</option> + <option value="mus_musculus_nzohlltj">mus_musculus_nzohlltj (Mouse NZO/HlLtJ) taxon_id: 10090</option> + <option value="mus_musculus_pwkphj">mus_musculus_pwkphj (Mouse PWK/PhJ) taxon_id: 39442</option> + <option value="mus_musculus_wsbeij">mus_musculus_wsbeij (Mouse WSB/EiJ) taxon_id: 10092</option> + <option value="mus_pahari">mus_pahari (Shrew mouse) taxon_id: 10093</option> + <option value="mus_spretus_spreteij">mus_spretus_spreteij (Algerian mouse) taxon_id: 10096</option> + <option value="mustela_putorius_furo">mustela_putorius_furo (Ferret) taxon_id: 9669</option> + <option value="myotis_lucifugus">myotis_lucifugus (Microbat) taxon_id: 59463</option> + <option value="nannospalax_galili">nannospalax_galili (Upper Galilee mountains blind mole rat) taxon_id: 1026970</option> + <option value="nomascus_leucogenys">nomascus_leucogenys (Gibbon) taxon_id: 61853</option> + <option value="notamacropus_eugenii">notamacropus_eugenii (Wallaby) taxon_id: 9315</option> + <option value="ochotona_princeps">ochotona_princeps (Pika) taxon_id: 9978</option> + <option value="octodon_degus">octodon_degus (Degu) taxon_id: 10160</option> + <option value="oreochromis_niloticus">oreochromis_niloticus (Tilapia) taxon_id: 8128</option> + <option value="ornithorhynchus_anatinus">ornithorhynchus_anatinus (Platypus) taxon_id: 9258</option> + <option value="oryctolagus_cuniculus">oryctolagus_cuniculus (Rabbit) taxon_id: 9986</option> + <option value="oryzias_latipes">oryzias_latipes (Medaka) taxon_id: 8090</option> + <option value="otolemur_garnettii">otolemur_garnettii (Bushbaby) taxon_id: 30611</option> + <option value="ovis_aries">ovis_aries (Sheep) taxon_id: 9940</option> + <option value="pan_troglodytes">pan_troglodytes (Chimpanzee) taxon_id: 9598</option> + <option value="papio_anubis">papio_anubis (Olive baboon) taxon_id: 9555</option> + <option value="pelodiscus_sinensis">pelodiscus_sinensis (Chinese softshell turtle) taxon_id: 13735</option> + <option value="peromyscus_maniculatus_bairdii">peromyscus_maniculatus_bairdii (Northern American deer mouse) taxon_id: 230844</option> + <option value="petromyzon_marinus">petromyzon_marinus (Lamprey) taxon_id: 7757</option> + <option value="poecilia_formosa">poecilia_formosa (Amazon molly) taxon_id: 48698</option> + <option value="pongo_abelii">pongo_abelii (Orangutan) taxon_id: 9601</option> + <option value="procavia_capensis">procavia_capensis (Hyrax) taxon_id: 9813</option> + <option value="pteropus_vampyrus">pteropus_vampyrus (Megabat) taxon_id: 132908</option> + <option value="rattus_norvegicus">rattus_norvegicus (Rat) taxon_id: 10116</option> + <option value="saccharomyces_cerevisiae">saccharomyces_cerevisiae (Saccharomyces cerevisiae) taxon_id: 4932</option> + <option value="sarcophilus_harrisii">sarcophilus_harrisii (Tasmanian devil) taxon_id: 9305</option> + <option value="sorex_araneus">sorex_araneus (Shrew) taxon_id: 42254</option> + <option value="sus_scrofa">sus_scrofa (Pig) taxon_id: 9823</option> + <option value="taeniopygia_guttata">taeniopygia_guttata (Zebra Finch) taxon_id: 59729</option> + <option value="takifugu_rubripes">takifugu_rubripes (Fugu) taxon_id: 31033</option> + <option value="tetraodon_nigroviridis">tetraodon_nigroviridis (Tetraodon) taxon_id: 99883</option> + <option value="tupaia_belangeri">tupaia_belangeri (Tree Shrew) taxon_id: 37347</option> + <option value="tursiops_truncatus">tursiops_truncatus (Dolphin) taxon_id: 9739</option> + <option value="vicugna_pacos">vicugna_pacos (Alpaca) taxon_id: 30538</option> + <option value="xenopus_tropicalis">xenopus_tropicalis (Xenopus) taxon_id: 8364</option> + <option value="xiphophorus_maculatus">xiphophorus_maculatus (Platyfish) taxon_id: 8083</option> + </xml> + <xml name="biotypes_help"> + <help><![CDATA[ +Example biotypes: +protein_coding, non_coding, pseudogene, nonsense_mediated_decay, non_stop_decay, +translated_processed_pseudogene, transcribed_processed_pseudogene, transcribed_unitary_pseudogene, transcribed_unprocessed_pseudogene, +polymorphic_pseudogene, processed_pseudogene, unprocessed_pseudogene, unitary_pseudogene, processed_transcript, +retained_intron, ccds_gene, sense_overlapping, sense_intronic, cdna_update, antisense, +LRG_gene, IG_C_gene, IG_D_gene, IG_J_gene, IG_LV_gene IG_V_gene, TR_C_gene, TR_D_gene, TR_J_gene, TR_V_gene, +IG_pseudogene, IG_C_pseudogene, IG_D_pseudogene, IG_J_pseudogene, IG_V_pseudogene, TR_J_pseudogene, TR_V_pseudogene, TEC, +ribozyme, RNase_P_RNA, guide_RNA, macro_lncRNA, bidirectional_promoter_lncRNA, 3prime_overlapping_ncRNA, antisense_RNA, vaultRNA, Y_RNA, SRP_RNA, RNase_MRP_RNA, IG_C_pseudogene, lncRNA, lincRNA, miRNA, snRNA, sRNA, telomerase_RNA, Mt_tRNA, Mt_rRNA, scaRNA, misc_RNA, rRNA, tRNA, scRNA, snoRNA, other + ]]></help> + </xml> +</macros>