Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_macros.xml @ 5:a5a3bdd0954b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
author galaxyp
date Mon, 11 Nov 2019 11:50:36 -0500
parents
children 3cb37af59360
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
1 <?xml version="1.0"?>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
2 <macros>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
3 <token name="@VERSION@">1.0.3</token>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
4 <xml name="citations">
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
5 <citations>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
6 <citation type="doi">10.1093/nar/gkv1248</citation>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
7 </citations>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
8 </xml>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
9 <xml name="requirements">
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
10 <requirements>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
11 <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
12 </requirements>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
13 </xml>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
14 <xml name="version_command">
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
15 <version_command>emapper.py --version</version_command>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
16 </xml>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
17 <xml name="data_manager_params">
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
18 <param name="test" type="hidden" value="false" />
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
19 <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database"/>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
20 <param argument="dbs" type="select" multiple="true" label="eggNOG HMM databases to download. If none are selected only diamond can be used'">
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
21 <option value="arch" selected="true">Archea arch_1 (arch)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
22 <option value="bact" selected="true">Bacteria bact_50 (bact)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
23 <option value="euk" selected="true">Eukaryote euk_500 (euk)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
24 <option value="NOG" selected="true">All organisms (NOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
25 <option value="aciNOG">Acidobacteria (aciNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
26 <option value="acidNOG">Acidobacteriia (acidNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
27 <option value="acoNOG">Aconoidasida (acoNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
28 <option value="actNOG">Actinobacteria (actNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
29 <option value="agaNOG">Agaricales (agaNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
30 <option value="agarNOG">Agaricomycetes (agarNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
31 <option value="apiNOG">Apicomplexa (apiNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
32 <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
33 <option value="aquNOG">Aquificae (aquNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
34 <option value="arNOG">Archaea (arNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
35 <option value="arcNOG">Archaeoglobi (arcNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
36 <option value="artNOG">Arthropoda (artNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
37 <option value="arthNOG">Arthrodermataceae (arthNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
38 <option value="ascNOG">Ascomycota (ascNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
39 <option value="aveNOG">Aves (aveNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
40 <option value="bacNOG">Bacilli (bacNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
41 <option value="bactNOG">Bacteria (bactNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
42 <option value="bacteNOG">Bacteroidia (bacteNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
43 <option value="basNOG">Basidiomycota (basNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
44 <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
45 <option value="biNOG">Bilateria (biNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
46 <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
47 <option value="braNOG">Brassicales (braNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
48 <option value="carNOG">Carnivora (carNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
49 <option value="chaNOG">Chaetomiaceae (chaNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
50 <option value="chlNOG">Chlorobi (chlNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
51 <option value="chlaNOG">Chlamydiae (chlaNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
52 <option value="chloNOG">Chloroflexi (chloNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
53 <option value="chlorNOG">Chloroflexi (chlorNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
54 <option value="chloroNOG">Chlorophyta (chloroNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
55 <option value="chorNOG">Chordata (chorNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
56 <option value="chrNOG">Chromadorea (chrNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
57 <option value="cloNOG">Clostridia (cloNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
58 <option value="cocNOG">Coccidia (cocNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
59 <option value="creNOG">Crenarchaeota (creNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
60 <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
61 <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
62 <option value="cytNOG">Cytophagia (cytNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
63 <option value="debNOG">Debaryomycetaceae (debNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
64 <option value="defNOG">Deferribacteres (defNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
65 <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
66 <option value="deiNOG">Deinococcusthermus (deiNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
67 <option value="delNOG">delta/epsilon (delNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
68 <option value="dipNOG">Diptera (dipNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
69 <option value="dotNOG">Dothideomycetes (dotNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
70 <option value="dproNOG">Proteobacteria_delta (dproNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
71 <option value="droNOG">Drosophilidae (droNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
72 <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
73 <option value="eryNOG">Erysipelotrichi (eryNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
74 <option value="euNOG">Eukaryotes (euNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
75 <option value="eurNOG">Euryarchaeota (eurNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
76 <option value="euroNOG">Eurotiomycetes (euroNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
77 <option value="eurotNOG">Eurotiales (eurotNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
78 <option value="fiNOG">Fishes (fiNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
79 <option value="firmNOG">Firmicutes (firmNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
80 <option value="flaNOG">Flavobacteriia (flaNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
81 <option value="fuNOG">Fungi (fuNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
82 <option value="fusoNOG">Fusobacteria (fusoNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
83 <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
84 <option value="haeNOG">Haemosporida (haeNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
85 <option value="halNOG">Halobacteria (halNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
86 <option value="homNOG">Hominidae (homNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
87 <option value="hymNOG">Hymenoptera (hymNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
88 <option value="hypNOG">Hypocreales (hypNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
89 <option value="inNOG">Insects (inNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
90 <option value="kinNOG">Kinetoplastida (kinNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
91 <option value="lepNOG">Lepidoptera (lepNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
92 <option value="lilNOG">Liliopsida (lilNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
93 <option value="maNOG">Mammals (maNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
94 <option value="magNOG">Magnaporthales (magNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
95 <option value="meNOG">Animals (meNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
96 <option value="metNOG">Methanobacteria (metNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
97 <option value="methNOG">Methanococci (methNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
98 <option value="methaNOG">Methanomicrobia (methaNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
99 <option value="necNOG">Nectriaceae (necNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
100 <option value="negNOG">Negativicutes (negNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
101 <option value="nemNOG">Nematodes (nemNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
102 <option value="onyNOG">Onygenales (onyNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
103 <option value="opiNOG">Opisthokonts (opiNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
104 <option value="perNOG">Peronosporales (perNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
105 <option value="plaNOG">Planctomycetes (plaNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
106 <option value="pleNOG">Pleosporales (pleNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
107 <option value="poaNOG">Poales (poaNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
108 <option value="prNOG">Primates (prNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
109 <option value="proNOG">Proteobacteria (proNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
110 <option value="rhaNOG">Rhabditida (rhaNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
111 <option value="roNOG">Rodents (roNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
112 <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
113 <option value="saccNOG">Saccharomycetes (saccNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
114 <option value="sorNOG">Sordariales (sorNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
115 <option value="sordNOG">Sordariomycetes (sordNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
116 <option value="sphNOG">Sphingobacteriia (sphNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
117 <option value="spiNOG">Spirochaetes (spiNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
118 <option value="spriNOG">Supraprimates (spriNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
119 <option value="strNOG">Streptophyta (strNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
120 <option value="synNOG">Synergistetes (synNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
121 <option value="tenNOG">Tenericutes (tenNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
122 <option value="thaNOG">Thaumarchaeota (thaNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
123 <option value="theNOG">Thermoplasmata (theNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
124 <option value="therNOG">Thermotogae (therNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
125 <option value="thermNOG">Thermococci (thermNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
126 <option value="treNOG">Tremellales (treNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
127 <option value="veNOG">Vertebrates (veNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
128 <option value="verNOG">Verrucomicrobia (verNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
129 <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
130 <option value="virNOG">Viridiplantae (virNOG)</option>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
131 </param>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
132 </xml>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
133 <xml name="data_manager_outputs">
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
134 <outputs>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
135 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
136 </outputs>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
137 </xml>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
138 <token name="@DOWNLOAD_CMD@"><![CDATA[
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
139 ## tool should set install_path
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
140 #if $test == 'true'
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
141 #import os.path
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
142 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally')
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
143 #end if
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
144 #if $dbs:
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
145 #set $eggnogdbs = ' '.join(str($dbs).split(','))
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
146 #else
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
147 #set $eggnogdbs = 'none'
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
148 #end if
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
149 mkdir -p '${install_path}' &&
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
150 download_eggnog_data.py
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
151 $diamond_database -y -q
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
152 #if $test == 'true'
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
153 -s
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
154 #end if
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
155 --data_dir '$install_path'
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
156 $eggnogdbs &&
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
157 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' --dbs '$dbs'
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
158 ]]></token>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
159 <xml name="data_manager_test">
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
160 <!--
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
161 <test>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
162 <param name="test" value="true"/>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
163 <param name="diamond_database" value="false"/>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
164 <param name="dbs" value="thaNOG"/>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
165 <output name="out_file">
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
166 <assert_contents>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
167 <has_text text="eggnog_mapper_db" />
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
168 </assert_contents>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
169 </output>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
170 </test>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
171 -->
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
172 </xml>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
173 </macros>