Mercurial > repos > galaxyp > data_manager_eggnog_mapper_abspath
comparison data_manager/eggnog_macros.xml @ 4:fcb8bdd124f4 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit e45c15081260025e470d23975ef5a734d3f8fc66"
author | galaxyp |
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date | Tue, 25 Jan 2022 13:51:24 +0000 |
parents | b711f5b6bd44 |
children | 81a286e4c5a2 |
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3:b711f5b6bd44 | 4:fcb8bdd124f4 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <macros> | 2 <macros> |
3 <token name="@VERSION@">2.0.1</token> | 3 <token name="@VERSION@">2.1.6</token> |
4 <token name="@EGGNOG_DB_VERSION@">2.0</token> | 4 <token name="@EGGNOG_DB_VERSION@">5.0.2</token> |
5 <!-- | 5 <!-- |
6 # Versionning is super confusing: | 6 # DB versionning was super confusing for eggnog-mapper 2.0.x: |
7 # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5) | 7 # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5) |
8 # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0) | 8 # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0) |
9 # db v4.5 are not compatible with eggnog-mapper 2.0 | 9 # (db v4.5 are not compatible with eggnog-mapper 2.0) |
10 # Starting with eggnog-mapper 2.1.* db versioning looks better: 2.1.0 requires db v5.0.2 | |
10 --> | 11 --> |
11 <token name="@IDX_VERSION@">2.0</token> | 12 <token name="@IDX_VERSION@">5.0.2</token> |
12 <xml name="citations"> | 13 <xml name="citations"> |
13 <citations> | 14 <citations> |
14 <citation type="doi">10.1093/nar/gkv1248</citation> | 15 <citation type="doi">10.1093/nar/gkv1248</citation> |
15 <citation type="doi">10.1093/molbev/msx148</citation> | 16 <citation type="doi">10.1093/molbev/msx148</citation> |
16 </citations> | 17 </citations> |
24 <version_command>emapper.py --version</version_command> | 25 <version_command>emapper.py --version</version_command> |
25 </xml> | 26 </xml> |
26 <xml name="data_manager_params"> | 27 <xml name="data_manager_params"> |
27 <param name="test" type="hidden" value="false" /> | 28 <param name="test" type="hidden" value="false" /> |
28 <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database" help="Takes ~9Gb, you most probably want it."/> | 29 <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database" help="Takes ~9Gb, you most probably want it."/> |
30 <param name="mmseqs_database" type="boolean" truevalue="-M" falsevalue="" checked="true" label="Install the MMseqs2 database" help="Required for mmseqs seed ortholog search mode. Takes ~11Gb, you most probably want it."/> | |
31 <param name="pfam_database" type="boolean" truevalue="-P" falsevalue="" checked="true" label="Install the Pfam database" help="Rquired for de novo annotation or realignment. Takes ~3Gb, you most probably want it."/> | |
29 </xml> | 32 </xml> |
30 <xml name="data_manager_outputs"> | 33 <xml name="data_manager_outputs"> |
31 <outputs> | 34 <outputs> |
32 <data name="out_file" format="data_manager_json" label="${tool.name}"/> | 35 <data name="out_file" format="data_manager_json" label="${tool.name}"/> |
33 </outputs> | 36 </outputs> |
38 #import os.path | 41 #import os.path |
39 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally') | 42 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally') |
40 #end if | 43 #end if |
41 mkdir -p '${install_path}' && | 44 mkdir -p '${install_path}' && |
42 download_eggnog_data.py | 45 download_eggnog_data.py |
43 $diamond_database -y -q | 46 $diamond_database $mmseqs_database $pfam_database -y -q |
44 #if $test == 'true' | 47 #if $test == 'true' |
45 -s | 48 -s |
46 #end if | 49 #end if |
47 --data_dir '$install_path' && | 50 --data_dir '$install_path' && |
48 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' | 51 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' |