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comparison eggnog_macros.xml @ 6:3cb37af59360 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
author galaxyp
date Sat, 05 Sep 2020 07:21:28 +0000
parents a5a3bdd0954b
children 4e4c6329f6cd
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5:a5a3bdd0954b 6:3cb37af59360
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@VERSION@">1.0.3</token> 3 <token name="@VERSION@">2.0.1</token>
4 <token name="@EGGNOG_DB_VERSION@">5.0</token>
4 <xml name="citations"> 5 <xml name="citations">
5 <citations> 6 <citations>
6 <citation type="doi">10.1093/nar/gkv1248</citation> 7 <citation type="doi">10.1093/nar/gkv1248</citation>
8 <citation type="doi">10.1093/molbev/msx148</citation>
7 </citations> 9 </citations>
8 </xml> 10 </xml>
9 <xml name="requirements"> 11 <xml name="requirements">
10 <requirements> 12 <requirements>
11 <requirement type="package" version="@VERSION@">eggnog-mapper</requirement> 13 <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
14 <xml name="version_command"> 16 <xml name="version_command">
15 <version_command>emapper.py --version</version_command> 17 <version_command>emapper.py --version</version_command>
16 </xml> 18 </xml>
17 <xml name="data_manager_params"> 19 <xml name="data_manager_params">
18 <param name="test" type="hidden" value="false" /> 20 <param name="test" type="hidden" value="false" />
19 <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database"/> 21 <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database" help="Takes ~9Gb, you most probably want it."/>
20 <param argument="dbs" type="select" multiple="true" label="eggNOG HMM databases to download. If none are selected only diamond can be used'">
21 <option value="arch" selected="true">Archea arch_1 (arch)</option>
22 <option value="bact" selected="true">Bacteria bact_50 (bact)</option>
23 <option value="euk" selected="true">Eukaryote euk_500 (euk)</option>
24 <option value="NOG" selected="true">All organisms (NOG)</option>
25 <option value="aciNOG">Acidobacteria (aciNOG)</option>
26 <option value="acidNOG">Acidobacteriia (acidNOG)</option>
27 <option value="acoNOG">Aconoidasida (acoNOG)</option>
28 <option value="actNOG">Actinobacteria (actNOG)</option>
29 <option value="agaNOG">Agaricales (agaNOG)</option>
30 <option value="agarNOG">Agaricomycetes (agarNOG)</option>
31 <option value="apiNOG">Apicomplexa (apiNOG)</option>
32 <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>
33 <option value="aquNOG">Aquificae (aquNOG)</option>
34 <option value="arNOG">Archaea (arNOG)</option>
35 <option value="arcNOG">Archaeoglobi (arcNOG)</option>
36 <option value="artNOG">Arthropoda (artNOG)</option>
37 <option value="arthNOG">Arthrodermataceae (arthNOG)</option>
38 <option value="ascNOG">Ascomycota (ascNOG)</option>
39 <option value="aveNOG">Aves (aveNOG)</option>
40 <option value="bacNOG">Bacilli (bacNOG)</option>
41 <option value="bactNOG">Bacteria (bactNOG)</option>
42 <option value="bacteNOG">Bacteroidia (bacteNOG)</option>
43 <option value="basNOG">Basidiomycota (basNOG)</option>
44 <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>
45 <option value="biNOG">Bilateria (biNOG)</option>
46 <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>
47 <option value="braNOG">Brassicales (braNOG)</option>
48 <option value="carNOG">Carnivora (carNOG)</option>
49 <option value="chaNOG">Chaetomiaceae (chaNOG)</option>
50 <option value="chlNOG">Chlorobi (chlNOG)</option>
51 <option value="chlaNOG">Chlamydiae (chlaNOG)</option>
52 <option value="chloNOG">Chloroflexi (chloNOG)</option>
53 <option value="chlorNOG">Chloroflexi (chlorNOG)</option>
54 <option value="chloroNOG">Chlorophyta (chloroNOG)</option>
55 <option value="chorNOG">Chordata (chorNOG)</option>
56 <option value="chrNOG">Chromadorea (chrNOG)</option>
57 <option value="cloNOG">Clostridia (cloNOG)</option>
58 <option value="cocNOG">Coccidia (cocNOG)</option>
59 <option value="creNOG">Crenarchaeota (creNOG)</option>
60 <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>
61 <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>
62 <option value="cytNOG">Cytophagia (cytNOG)</option>
63 <option value="debNOG">Debaryomycetaceae (debNOG)</option>
64 <option value="defNOG">Deferribacteres (defNOG)</option>
65 <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>
66 <option value="deiNOG">Deinococcusthermus (deiNOG)</option>
67 <option value="delNOG">delta/epsilon (delNOG)</option>
68 <option value="dipNOG">Diptera (dipNOG)</option>
69 <option value="dotNOG">Dothideomycetes (dotNOG)</option>
70 <option value="dproNOG">Proteobacteria_delta (dproNOG)</option>
71 <option value="droNOG">Drosophilidae (droNOG)</option>
72 <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option>
73 <option value="eryNOG">Erysipelotrichi (eryNOG)</option>
74 <option value="euNOG">Eukaryotes (euNOG)</option>
75 <option value="eurNOG">Euryarchaeota (eurNOG)</option>
76 <option value="euroNOG">Eurotiomycetes (euroNOG)</option>
77 <option value="eurotNOG">Eurotiales (eurotNOG)</option>
78 <option value="fiNOG">Fishes (fiNOG)</option>
79 <option value="firmNOG">Firmicutes (firmNOG)</option>
80 <option value="flaNOG">Flavobacteriia (flaNOG)</option>
81 <option value="fuNOG">Fungi (fuNOG)</option>
82 <option value="fusoNOG">Fusobacteria (fusoNOG)</option>
83 <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option>
84 <option value="haeNOG">Haemosporida (haeNOG)</option>
85 <option value="halNOG">Halobacteria (halNOG)</option>
86 <option value="homNOG">Hominidae (homNOG)</option>
87 <option value="hymNOG">Hymenoptera (hymNOG)</option>
88 <option value="hypNOG">Hypocreales (hypNOG)</option>
89 <option value="inNOG">Insects (inNOG)</option>
90 <option value="kinNOG">Kinetoplastida (kinNOG)</option>
91 <option value="lepNOG">Lepidoptera (lepNOG)</option>
92 <option value="lilNOG">Liliopsida (lilNOG)</option>
93 <option value="maNOG">Mammals (maNOG)</option>
94 <option value="magNOG">Magnaporthales (magNOG)</option>
95 <option value="meNOG">Animals (meNOG)</option>
96 <option value="metNOG">Methanobacteria (metNOG)</option>
97 <option value="methNOG">Methanococci (methNOG)</option>
98 <option value="methaNOG">Methanomicrobia (methaNOG)</option>
99 <option value="necNOG">Nectriaceae (necNOG)</option>
100 <option value="negNOG">Negativicutes (negNOG)</option>
101 <option value="nemNOG">Nematodes (nemNOG)</option>
102 <option value="onyNOG">Onygenales (onyNOG)</option>
103 <option value="opiNOG">Opisthokonts (opiNOG)</option>
104 <option value="perNOG">Peronosporales (perNOG)</option>
105 <option value="plaNOG">Planctomycetes (plaNOG)</option>
106 <option value="pleNOG">Pleosporales (pleNOG)</option>
107 <option value="poaNOG">Poales (poaNOG)</option>
108 <option value="prNOG">Primates (prNOG)</option>
109 <option value="proNOG">Proteobacteria (proNOG)</option>
110 <option value="rhaNOG">Rhabditida (rhaNOG)</option>
111 <option value="roNOG">Rodents (roNOG)</option>
112 <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>
113 <option value="saccNOG">Saccharomycetes (saccNOG)</option>
114 <option value="sorNOG">Sordariales (sorNOG)</option>
115 <option value="sordNOG">Sordariomycetes (sordNOG)</option>
116 <option value="sphNOG">Sphingobacteriia (sphNOG)</option>
117 <option value="spiNOG">Spirochaetes (spiNOG)</option>
118 <option value="spriNOG">Supraprimates (spriNOG)</option>
119 <option value="strNOG">Streptophyta (strNOG)</option>
120 <option value="synNOG">Synergistetes (synNOG)</option>
121 <option value="tenNOG">Tenericutes (tenNOG)</option>
122 <option value="thaNOG">Thaumarchaeota (thaNOG)</option>
123 <option value="theNOG">Thermoplasmata (theNOG)</option>
124 <option value="therNOG">Thermotogae (therNOG)</option>
125 <option value="thermNOG">Thermococci (thermNOG)</option>
126 <option value="treNOG">Tremellales (treNOG)</option>
127 <option value="veNOG">Vertebrates (veNOG)</option>
128 <option value="verNOG">Verrucomicrobia (verNOG)</option>
129 <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>
130 <option value="virNOG">Viridiplantae (virNOG)</option>
131 </param>
132 </xml> 22 </xml>
133 <xml name="data_manager_outputs"> 23 <xml name="data_manager_outputs">
134 <outputs> 24 <outputs>
135 <data name="out_file" format="data_manager_json" label="${tool.name}"/> 25 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
136 </outputs> 26 </outputs>
139 ## tool should set install_path 29 ## tool should set install_path
140 #if $test == 'true' 30 #if $test == 'true'
141 #import os.path 31 #import os.path
142 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally') 32 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally')
143 #end if 33 #end if
144 #if $dbs:
145 #set $eggnogdbs = ' '.join(str($dbs).split(','))
146 #else
147 #set $eggnogdbs = 'none'
148 #end if
149 mkdir -p '${install_path}' && 34 mkdir -p '${install_path}' &&
150 download_eggnog_data.py 35 download_eggnog_data.py
151 $diamond_database -y -q 36 $diamond_database -y -q
152 #if $test == 'true' 37 #if $test == 'true'
153 -s 38 -s
154 #end if 39 #end if
155 --data_dir '$install_path' 40 --data_dir '$install_path' &&
156 $eggnogdbs && 41 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path'
157 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' --dbs '$dbs'
158 ]]></token> 42 ]]></token>
159 <xml name="data_manager_test"> 43 <xml name="data_manager_test">
160 <!--
161 <test> 44 <test>
162 <param name="test" value="true"/> 45 <param name="test" value="true"/>
163 <param name="diamond_database" value="false"/> 46 <param name="diamond_database" value="true"/>
164 <param name="dbs" value="thaNOG"/> 47 <yield />
165 <output name="out_file"> 48 <output name="out_file">
166 <assert_contents> 49 <assert_contents>
167 <has_text text="eggnog_mapper_db" /> 50 <has_text text="eggnog_mapper_db" />
51 <has_text text="@EGGNOG_DB_VERSION@" />
168 </assert_contents> 52 </assert_contents>
169 </output> 53 </output>
170 </test> 54 </test>
171 -->
172 </xml> 55 </xml>
173 </macros> 56 </macros>