Mercurial > repos > galaxyp > eggnog_mapper

comparison eggnog_macros.xml @ 8:96cac424c870 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
author galaxyp
date Tue, 25 Jan 2022 13:51:50 +0000
parents 4e4c6329f6cd
children 5a30ae278db0
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7:4e4c6329f6cd 8:96cac424c870
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'