Mercurial > repos > galaxyp > retrieve_ensembl_bed

annotate macros.xml @ 0:da1b538b87e5 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
author galaxyp
date Mon, 22 Jan 2018 13:13:47 -0500
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da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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1 <macros>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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2 <xml name="bedutil_requirements">
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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3 <requirement type="package" version="1.62">biopython</requirement>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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4 </xml>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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5 <xml name="ensembl_requirements">
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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6 <requirement type="package" version="0.4.10">requests-cache</requirement>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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7 </xml>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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8 <xml name="twobit_requirements">
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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9 <requirement type="package" version="3.1.4">twobitreader</requirement>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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10 </xml>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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11 <xml name="species_options">
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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12 <option value="homo_sapiens">homo_sapiens (Human) taxon_id: 9606</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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13 <option value="mus_musculus">mus_musculus (Mouse) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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14 <option value="ailuropoda_melanoleuca">ailuropoda_melanoleuca (Panda) taxon_id: 9646</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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15 <option value="anas_platyrhynchos">anas_platyrhynchos (Duck) taxon_id: 8839</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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16 <option value="anolis_carolinensis">anolis_carolinensis (Anole lizard) taxon_id: 28377</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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17 <option value="astyanax_mexicanus">astyanax_mexicanus (Cave fish) taxon_id: 7994</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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18 <option value="bos_taurus">bos_taurus (Cow) taxon_id: 9913</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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19 <option value="caenorhabditis_elegans">caenorhabditis_elegans (Caenorhabditis elegans) taxon_id: 6239</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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20 <option value="callithrix_jacchus">callithrix_jacchus (Marmoset) taxon_id: 9483</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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21 <option value="canis_familiaris">canis_familiaris (Dog) taxon_id: 9615</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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22 <option value="carlito_syrichta">carlito_syrichta (Tarsier) taxon_id: 1868482</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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23 <option value="cavia_aperea">cavia_aperea (Brazilian guinea pig) taxon_id: 37548</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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24 <option value="cavia_porcellus">cavia_porcellus (Guinea Pig) taxon_id: 10141</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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25 <option value="chinchilla_lanigera">chinchilla_lanigera (Long-tailed chinchilla) taxon_id: 34839</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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26 <option value="chlorocebus_sabaeus">chlorocebus_sabaeus (Vervet-AGM) taxon_id: 60711</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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27 <option value="choloepus_hoffmanni">choloepus_hoffmanni (Sloth) taxon_id: 9358</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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28 <option value="ciona_intestinalis">ciona_intestinalis (C.intestinalis) taxon_id: 7719</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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29 <option value="ciona_savignyi">ciona_savignyi (C.savignyi) taxon_id: 51511</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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30 <option value="cricetulus_griseus_chok1gshd">cricetulus_griseus_chok1gshd (Chinese hamster CHOK1GS) taxon_id: 10029</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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31 <option value="cricetulus_griseus_crigri">cricetulus_griseus_crigri (Chinese hamster CriGri) taxon_id: 10029</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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32 <option value="danio_rerio">danio_rerio (Zebrafish) taxon_id: 7955</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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33 <option value="dasypus_novemcinctus">dasypus_novemcinctus (Armadillo) taxon_id: 9361</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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34 <option value="dipodomys_ordii">dipodomys_ordii (Kangaroo rat) taxon_id: 10020</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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35 <option value="drosophila_melanogaster">drosophila_melanogaster (Fruitfly) taxon_id: 7227</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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36 <option value="echinops_telfairi">echinops_telfairi (Lesser hedgehog tenrec) taxon_id: 9371</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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37 <option value="equus_caballus">equus_caballus (Horse) taxon_id: 9796</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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38 <option value="erinaceus_europaeus">erinaceus_europaeus (Hedgehog) taxon_id: 9365</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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39 <option value="felis_catus">felis_catus (Cat) taxon_id: 9685</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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40 <option value="ficedula_albicollis">ficedula_albicollis (Flycatcher) taxon_id: 59894</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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41 <option value="fukomys_damarensis">fukomys_damarensis (Damara mole rat) taxon_id: 885580</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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42 <option value="gadus_morhua">gadus_morhua (Cod) taxon_id: 8049</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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43 <option value="gallus_gallus">gallus_gallus (Chicken) taxon_id: 9031</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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44 <option value="gasterosteus_aculeatus">gasterosteus_aculeatus (Stickleback) taxon_id: 69293</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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45 <option value="gorilla_gorilla">gorilla_gorilla (Gorilla) taxon_id: 9595</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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46 <option value="heterocephalus_glaber_female">heterocephalus_glaber_female (Naked mole-rat female) taxon_id: 10181</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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47 <option value="heterocephalus_glaber_male">heterocephalus_glaber_male (Naked mole-rat male) taxon_id: 10181</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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48 <option value="ictidomys_tridecemlineatus">ictidomys_tridecemlineatus (Squirrel) taxon_id: 43179</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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49 <option value="jaculus_jaculus">jaculus_jaculus (Lesser Egyptian jerboa) taxon_id: 51337</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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50 <option value="latimeria_chalumnae">latimeria_chalumnae (Coelacanth) taxon_id: 7897</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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51 <option value="lepisosteus_oculatus">lepisosteus_oculatus (Spotted gar) taxon_id: 7918</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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52 <option value="loxodonta_africana">loxodonta_africana (Elephant) taxon_id: 9785</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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53 <option value="macaca_mulatta">macaca_mulatta (Macaque) taxon_id: 9544</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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54 <option value="meleagris_gallopavo">meleagris_gallopavo (Turkey) taxon_id: 9103</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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55 <option value="mesocricetus_auratus">mesocricetus_auratus (Golden Hamster) taxon_id: 10036</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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56 <option value="microcebus_murinus">microcebus_murinus (Mouse Lemur) taxon_id: 30608</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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57 <option value="microtus_ochrogaster">microtus_ochrogaster (Prairie vole) taxon_id: 79684</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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58 <option value="monodelphis_domestica">monodelphis_domestica (Opossum) taxon_id: 13616</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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59 <option value="mus_caroli">mus_caroli (Ryukyu mouse) taxon_id: 10089</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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60 <option value="mus_musculus_129s1svimj">mus_musculus_129s1svimj (Mouse 129S1/SvImJ) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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61 <option value="mus_musculus_aj">mus_musculus_aj (Mouse A/J) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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62 <option value="mus_musculus_akrj">mus_musculus_akrj (Mouse AKR/J) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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63 <option value="mus_musculus_balbcj">mus_musculus_balbcj (Mouse BALB/cJ) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
64 <option value="mus_musculus_c3hhej">mus_musculus_c3hhej (Mouse C3H/HeJ) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
65 <option value="mus_musculus_c57bl6nj">mus_musculus_c57bl6nj (Mouse C57BL/6NJ) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
66 <option value="mus_musculus_casteij">mus_musculus_casteij (Mouse CAST/EiJ) taxon_id: 10091</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
67 <option value="mus_musculus_cbaj">mus_musculus_cbaj (Mouse CBA/J) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
68 <option value="mus_musculus_dba2j">mus_musculus_dba2j (Mouse DBA/2J) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
69 <option value="mus_musculus_fvbnj">mus_musculus_fvbnj (Mouse FVB/NJ) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
70 <option value="mus_musculus_lpj">mus_musculus_lpj (Mouse LP/J) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
71 <option value="mus_musculus_nodshiltj">mus_musculus_nodshiltj (Mouse NOD/ShiLtJ) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
72 <option value="mus_musculus_nzohlltj">mus_musculus_nzohlltj (Mouse NZO/HlLtJ) taxon_id: 10090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
73 <option value="mus_musculus_pwkphj">mus_musculus_pwkphj (Mouse PWK/PhJ) taxon_id: 39442</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
74 <option value="mus_musculus_wsbeij">mus_musculus_wsbeij (Mouse WSB/EiJ) taxon_id: 10092</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
75 <option value="mus_pahari">mus_pahari (Shrew mouse) taxon_id: 10093</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
76 <option value="mus_spretus_spreteij">mus_spretus_spreteij (Algerian mouse) taxon_id: 10096</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
77 <option value="mustela_putorius_furo">mustela_putorius_furo (Ferret) taxon_id: 9669</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
78 <option value="myotis_lucifugus">myotis_lucifugus (Microbat) taxon_id: 59463</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
79 <option value="nannospalax_galili">nannospalax_galili (Upper Galilee mountains blind mole rat) taxon_id: 1026970</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
80 <option value="nomascus_leucogenys">nomascus_leucogenys (Gibbon) taxon_id: 61853</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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81 <option value="notamacropus_eugenii">notamacropus_eugenii (Wallaby) taxon_id: 9315</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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82 <option value="ochotona_princeps">ochotona_princeps (Pika) taxon_id: 9978</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
83 <option value="octodon_degus">octodon_degus (Degu) taxon_id: 10160</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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84 <option value="oreochromis_niloticus">oreochromis_niloticus (Tilapia) taxon_id: 8128</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
85 <option value="ornithorhynchus_anatinus">ornithorhynchus_anatinus (Platypus) taxon_id: 9258</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
86 <option value="oryctolagus_cuniculus">oryctolagus_cuniculus (Rabbit) taxon_id: 9986</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
87 <option value="oryzias_latipes">oryzias_latipes (Medaka) taxon_id: 8090</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
88 <option value="otolemur_garnettii">otolemur_garnettii (Bushbaby) taxon_id: 30611</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
89 <option value="ovis_aries">ovis_aries (Sheep) taxon_id: 9940</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
90 <option value="pan_troglodytes">pan_troglodytes (Chimpanzee) taxon_id: 9598</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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91 <option value="papio_anubis">papio_anubis (Olive baboon) taxon_id: 9555</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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92 <option value="pelodiscus_sinensis">pelodiscus_sinensis (Chinese softshell turtle) taxon_id: 13735</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
93 <option value="peromyscus_maniculatus_bairdii">peromyscus_maniculatus_bairdii (Northern American deer mouse) taxon_id: 230844</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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94 <option value="petromyzon_marinus">petromyzon_marinus (Lamprey) taxon_id: 7757</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
95 <option value="poecilia_formosa">poecilia_formosa (Amazon molly) taxon_id: 48698</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
96 <option value="pongo_abelii">pongo_abelii (Orangutan) taxon_id: 9601</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
diff changeset
97 <option value="procavia_capensis">procavia_capensis (Hyrax) taxon_id: 9813</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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98 <option value="pteropus_vampyrus">pteropus_vampyrus (Megabat) taxon_id: 132908</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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99 <option value="rattus_norvegicus">rattus_norvegicus (Rat) taxon_id: 10116</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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100 <option value="saccharomyces_cerevisiae">saccharomyces_cerevisiae (Saccharomyces cerevisiae) taxon_id: 4932</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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101 <option value="sarcophilus_harrisii">sarcophilus_harrisii (Tasmanian devil) taxon_id: 9305</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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102 <option value="sorex_araneus">sorex_araneus (Shrew) taxon_id: 42254</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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103 <option value="sus_scrofa">sus_scrofa (Pig) taxon_id: 9823</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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104 <option value="taeniopygia_guttata">taeniopygia_guttata (Zebra Finch) taxon_id: 59729</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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105 <option value="takifugu_rubripes">takifugu_rubripes (Fugu) taxon_id: 31033</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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106 <option value="tetraodon_nigroviridis">tetraodon_nigroviridis (Tetraodon) taxon_id: 99883</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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107 <option value="tupaia_belangeri">tupaia_belangeri (Tree Shrew) taxon_id: 37347</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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108 <option value="tursiops_truncatus">tursiops_truncatus (Dolphin) taxon_id: 9739</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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109 <option value="vicugna_pacos">vicugna_pacos (Alpaca) taxon_id: 30538</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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110 <option value="xenopus_tropicalis">xenopus_tropicalis (Xenopus) taxon_id: 8364</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
parents:
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111 <option value="xiphophorus_maculatus">xiphophorus_maculatus (Platyfish) taxon_id: 8083</option>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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112 </xml>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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113 <xml name="biotypes_help">
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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114 <help><![CDATA[
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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115 Example biotypes:
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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116 protein_coding, non_coding, pseudogene, nonsense_mediated_decay, non_stop_decay,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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117 translated_processed_pseudogene, transcribed_processed_pseudogene, transcribed_unitary_pseudogene, transcribed_unprocessed_pseudogene,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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118 polymorphic_pseudogene, processed_pseudogene, unprocessed_pseudogene, unitary_pseudogene, processed_transcript,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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119 retained_intron, ccds_gene, sense_overlapping, sense_intronic, cdna_update, antisense,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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120 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,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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121 IG_pseudogene, IG_C_pseudogene, IG_D_pseudogene, IG_J_pseudogene, IG_V_pseudogene, TR_J_pseudogene, TR_V_pseudogene, TEC,
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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122 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
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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123 ]]></help>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
galaxyp
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124 </xml>
da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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125 </macros>