Mercurial > repos > galaxyp > data_manager_eggnog_mapper

annotate data_manager/eggnog_macros.xml @ 2:55cb477ec52c 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_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
author galaxyp
date Tue, 25 Jan 2022 13:49:07 +0000
parents a0625e4f566b
children 4a7444e92ad5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
1 <?xml version="1.0"?>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
2 <macros>
2
55cb477ec52c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 1
diff changeset
3 <token name="@VERSION@">2.1.6</token>
55cb477ec52c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 1
diff changeset
4 <token name="@EGGNOG_DB_VERSION@">5.0.2</token>
1
a0625e4f566b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 0
diff changeset
5 <!--
2
55cb477ec52c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 1
diff changeset
6 # DB versionning was super confusing for eggnog-mapper 2.0.x:
1
a0625e4f566b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 0
diff changeset
7 # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5)
2
55cb477ec52c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 1
diff changeset
8 # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0)
55cb477ec52c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 1
diff changeset
9 # (db v4.5 are not compatible with eggnog-mapper 2.0)
55cb477ec52c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 1
diff changeset
10 # Starting with eggnog-mapper 2.1.* db versioning looks better: 2.1.0 requires db v5.0.2
1
a0625e4f566b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 0
diff changeset
11 -->
2
55cb477ec52c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 1
diff changeset
12 <token name="@IDX_VERSION@">5.0.2</token>
0
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
13 <xml name="citations">
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
14 <citations>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
15 <citation type="doi">10.1093/nar/gkv1248</citation>
1
a0625e4f566b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 0
diff changeset
16 <citation type="doi">10.1093/molbev/msx148</citation>
0
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
17 </citations>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
18 </xml>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
19 <xml name="requirements">
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
20 <requirements>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
21 <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
22 </requirements>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
23 </xml>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
24 <xml name="version_command">
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
25 <version_command>emapper.py --version</version_command>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
26 </xml>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
27 <xml name="data_manager_params">
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
28 <param name="test" type="hidden" value="false" />
1
a0625e4f566b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 0
diff changeset
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."/>
2
55cb477ec52c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 1
diff changeset
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."/>
55cb477ec52c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 1
diff changeset
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."/>
0
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
32 </xml>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
33 <xml name="data_manager_outputs">
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
34 <outputs>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
35 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
36 </outputs>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
37 </xml>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
38 <token name="@DOWNLOAD_CMD@"><![CDATA[
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
39 ## tool should set install_path
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
40 #if $test == 'true'
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
41 #import os.path
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
42 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally')
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
43 #end if
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
44 mkdir -p '${install_path}' &&
1
a0625e4f566b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 0
diff changeset
45 download_eggnog_data.py
2
55cb477ec52c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 1
diff changeset
46 $diamond_database $mmseqs_database $pfam_database -y -q
0
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
47 #if $test == 'true'
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
48 -s
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
49 #end if
1
a0625e4f566b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 0
diff changeset
50 --data_dir '$install_path' &&
a0625e4f566b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 0
diff changeset
51 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path'
0
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
52 ]]></token>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
53 <xml name="data_manager_test">
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
54 <test>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
55 <param name="test" value="true"/>
1
a0625e4f566b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 0
diff changeset
56 <param name="diamond_database" value="true"/>
a0625e4f566b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 0
diff changeset
57 <yield />
0
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
58 <output name="out_file">
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
59 <assert_contents>
1
a0625e4f566b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 0
diff changeset
60 <has_text text="eggnog_mapper_db_versioned" />
a0625e4f566b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 0
diff changeset
61 <has_text text="@EGGNOG_DB_VERSION@" />
0
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
62 </assert_contents>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
63 </output>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
64 </test>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
65 </xml>
bcb556946648 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents:
diff changeset
66 </macros>