Mercurial > repos > jjohnson > eggnog_mapper

annotate eggnog_macros.xml @ 8:c2d4738c3282 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 288c3043b10594647e9f6e5de56bf98a38779f75-dirty
author jjohnson
date Fri, 08 Nov 2019 14:40:14 -0500
parents 69ab06b777c6
children
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5
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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1 <?xml version="1.0"?>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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2 <macros>
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3 <token name="@VERSION@">1.0.3</token>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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4 <xml name="citations">
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5 <citations>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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6 <citation type="doi">10.1093/nar/gkv1248</citation>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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7 </citations>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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8 </xml>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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9 <xml name="requirements">
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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10 <requirements>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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11 <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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12 </requirements>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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13 </xml>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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14 <xml name="version_command">
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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15 <version_command>emapper.py --version</version_command>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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16 </xml>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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17 <xml name="data_manager_params">
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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18 <param name="test" type="hidden" value="false" />
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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19 <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database"/>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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20 <param argument="dbs" type="select" multiple="true" label="eggNOG HMM databases to download. If none are selected only diamond can be used'">
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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21 <option value="arch" selected="true">Archea arch_1 (arch)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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22 <option value="bact" selected="true">Bacteria bact_50 (bact)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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23 <option value="euk" selected="true">Eukaryote euk_500 (euk)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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24 <option value="NOG" selected="true">All organisms (NOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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25 <option value="aciNOG">Acidobacteria (aciNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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26 <option value="acidNOG">Acidobacteriia (acidNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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27 <option value="acoNOG">Aconoidasida (acoNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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28 <option value="actNOG">Actinobacteria (actNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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29 <option value="agaNOG">Agaricales (agaNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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30 <option value="agarNOG">Agaricomycetes (agarNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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31 <option value="apiNOG">Apicomplexa (apiNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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32 <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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33 <option value="aquNOG">Aquificae (aquNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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34 <option value="arNOG">Archaea (arNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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35 <option value="arcNOG">Archaeoglobi (arcNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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36 <option value="artNOG">Arthropoda (artNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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37 <option value="arthNOG">Arthrodermataceae (arthNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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38 <option value="ascNOG">Ascomycota (ascNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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39 <option value="aveNOG">Aves (aveNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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40 <option value="bacNOG">Bacilli (bacNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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41 <option value="bactNOG">Bacteria (bactNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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42 <option value="bacteNOG">Bacteroidia (bacteNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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43 <option value="basNOG">Basidiomycota (basNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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44 <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>
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45 <option value="biNOG">Bilateria (biNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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46 <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>
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47 <option value="braNOG">Brassicales (braNOG)</option>
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48 <option value="carNOG">Carnivora (carNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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49 <option value="chaNOG">Chaetomiaceae (chaNOG)</option>
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50 <option value="chlNOG">Chlorobi (chlNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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51 <option value="chlaNOG">Chlamydiae (chlaNOG)</option>
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52 <option value="chloNOG">Chloroflexi (chloNOG)</option>
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53 <option value="chlorNOG">Chloroflexi (chlorNOG)</option>
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54 <option value="chloroNOG">Chlorophyta (chloroNOG)</option>
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55 <option value="chorNOG">Chordata (chorNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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56 <option value="chrNOG">Chromadorea (chrNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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57 <option value="cloNOG">Clostridia (cloNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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58 <option value="cocNOG">Coccidia (cocNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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59 <option value="creNOG">Crenarchaeota (creNOG)</option>
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60 <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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61 <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>
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62 <option value="cytNOG">Cytophagia (cytNOG)</option>
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63 <option value="debNOG">Debaryomycetaceae (debNOG)</option>
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64 <option value="defNOG">Deferribacteres (defNOG)</option>
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65 <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>
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66 <option value="deiNOG">Deinococcusthermus (deiNOG)</option>
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67 <option value="delNOG">delta/epsilon (delNOG)</option>
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68 <option value="dipNOG">Diptera (dipNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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69 <option value="dotNOG">Dothideomycetes (dotNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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70 <option value="dproNOG">Proteobacteria_delta (dproNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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71 <option value="droNOG">Drosophilidae (droNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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72 <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option>
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73 <option value="eryNOG">Erysipelotrichi (eryNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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74 <option value="euNOG">Eukaryotes (euNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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75 <option value="eurNOG">Euryarchaeota (eurNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
76 <option value="euroNOG">Eurotiomycetes (euroNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
77 <option value="eurotNOG">Eurotiales (eurotNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
78 <option value="fiNOG">Fishes (fiNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
79 <option value="firmNOG">Firmicutes (firmNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
80 <option value="flaNOG">Flavobacteriia (flaNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
81 <option value="fuNOG">Fungi (fuNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
82 <option value="fusoNOG">Fusobacteria (fusoNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
83 <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
84 <option value="haeNOG">Haemosporida (haeNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
85 <option value="halNOG">Halobacteria (halNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
86 <option value="homNOG">Hominidae (homNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
87 <option value="hymNOG">Hymenoptera (hymNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
diff changeset
88 <option value="hypNOG">Hypocreales (hypNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
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89 <option value="inNOG">Insects (inNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
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90 <option value="kinNOG">Kinetoplastida (kinNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
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91 <option value="lepNOG">Lepidoptera (lepNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
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92 <option value="lilNOG">Liliopsida (lilNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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93 <option value="maNOG">Mammals (maNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
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94 <option value="magNOG">Magnaporthales (magNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
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95 <option value="meNOG">Animals (meNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
parents:
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96 <option value="metNOG">Methanobacteria (metNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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97 <option value="methNOG">Methanococci (methNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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98 <option value="methaNOG">Methanomicrobia (methaNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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99 <option value="necNOG">Nectriaceae (necNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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100 <option value="negNOG">Negativicutes (negNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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101 <option value="nemNOG">Nematodes (nemNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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102 <option value="onyNOG">Onygenales (onyNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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103 <option value="opiNOG">Opisthokonts (opiNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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104 <option value="perNOG">Peronosporales (perNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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105 <option value="plaNOG">Planctomycetes (plaNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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106 <option value="pleNOG">Pleosporales (pleNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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107 <option value="poaNOG">Poales (poaNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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108 <option value="prNOG">Primates (prNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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109 <option value="proNOG">Proteobacteria (proNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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110 <option value="rhaNOG">Rhabditida (rhaNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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111 <option value="roNOG">Rodents (roNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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112 <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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113 <option value="saccNOG">Saccharomycetes (saccNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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114 <option value="sorNOG">Sordariales (sorNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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115 <option value="sordNOG">Sordariomycetes (sordNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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116 <option value="sphNOG">Sphingobacteriia (sphNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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117 <option value="spiNOG">Spirochaetes (spiNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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118 <option value="spriNOG">Supraprimates (spriNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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119 <option value="strNOG">Streptophyta (strNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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120 <option value="synNOG">Synergistetes (synNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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121 <option value="tenNOG">Tenericutes (tenNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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122 <option value="thaNOG">Thaumarchaeota (thaNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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123 <option value="theNOG">Thermoplasmata (theNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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124 <option value="therNOG">Thermotogae (therNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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125 <option value="thermNOG">Thermococci (thermNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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126 <option value="treNOG">Tremellales (treNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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127 <option value="veNOG">Vertebrates (veNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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128 <option value="verNOG">Verrucomicrobia (verNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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129 <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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130 <option value="virNOG">Viridiplantae (virNOG)</option>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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131 </param>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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132 </xml>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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133 <xml name="data_manager_outputs">
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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134 <outputs>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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135 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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136 </outputs>
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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137 </xml>
7
69ab06b777c6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
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diff changeset
138 <token name="@DOWNLOAD_CMD@"><![CDATA[
5
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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139 ## tool should set install_path
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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140 #if $test == 'true'
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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141 #import os.path
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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142 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally')
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
jjohnson
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143 #end if
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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144 #if $dbs:
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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145 #set $eggnogdbs = ' '.join(str($dbs).split(','))
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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146 #else
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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147 #set $eggnogdbs = 'none'
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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148 #end if
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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149 mkdir -p '${install_path}' &&
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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150 download_eggnog_data.py
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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151 $diamond_database -y -q
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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152 #if $test == 'true'
a093b9061498 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 525985820e3426e13869da264197fd3e8ce8bc01
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153 -s
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154 #end if
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155 --data_dir '$install_path'
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156 $eggnogdbs &&
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157 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' --dbs '$dbs'
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158 ]]></token>
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159 <xml name="data_manager_test">
7
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160 <!--
5
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161 <test>
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162 <param name="test" value="true"/>
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163 <param name="diamond_database" value="false"/>
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164 <param name="dbs" value="thaNOG"/>
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165 <output name="out_file">
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166 <assert_contents>
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167 <has_text text="eggnog_mapper_db" />
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168 </assert_contents>
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169 </output>
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170 </test>
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171 -->
5
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172 </xml>
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173 </macros>