annotate eggnog_mapper.xml @ 14:d9c3016f7283 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 192779247c3385704ebd98a2cc47a210fb1f4d0c
author galaxyp
date Thu, 07 Sep 2023 18:51:23 +0000
parents 844fa988236b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
2 <description>functional sequence annotation by orthology</description>
4
2667d24b58a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 16eed6250e9a238dacfa4c775d9db4e232817b99
galaxyp
parents: 3
diff changeset
3 <macros>
5
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents: 4
diff changeset
4 <import>eggnog_macros.xml</import>
4
2667d24b58a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 16eed6250e9a238dacfa4c775d9db4e232817b99
galaxyp
parents: 3
diff changeset
5 </macros>
5
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents: 4
diff changeset
6 <expand macro="requirements"/>
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents: 4
diff changeset
7 <expand macro="version_command"/>
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
8 <command detect_errors="aggressive"><![CDATA[
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
9 @MERGE_ANNOTATIONS@
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
10
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
11 emapper.py
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
12 @DB_TOKEN@
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
13 @ORTHO_SEARCH_TOKEN@
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
14 #if $annotation_options.no_annot == "--no_annot"
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
15 --no_annot
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
16 #else
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
17 @ANNOTATION_TOKEN@
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
18 #end if
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
19 $output_options.no_file_comments
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
20 $output_options.report_orthologs
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
21 $output_options.md5
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
22 --output='results'
1
3c7c9396daaa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9505f2a447df1bcd46ceca7b5ddb532a2f8a1cd1
galaxyp
parents: 0
diff changeset
23 --cpu "\${GALAXY_SLOTS:-4}"
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
24 --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
25 --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
26 ]]></command>
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
27 <inputs>
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
28 <expand macro="db_macro"/>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
29 <expand macro="ortho_full_macro"/>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
30 <conditional name="annotation_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
31 <param argument="--no_annot" type="select" label="Annotate seed orthologs">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
32 <option value="">Yes</option>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
33 <option value="--no_annot">No</option>
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
34 </param>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
35 <when value="">
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
36 <expand macro="annotation_options_macro"/>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
37 </when>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
38 <when value="--no_annot"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
39 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
40
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
41 <expand macro="output_options_annotate_macro"/>
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
42 </inputs>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
43 <outputs>
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
44 <expand macro="ortho_search_output_macro"/>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
45 <expand macro="annotation_output_macro">
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
46 <filter>annotation_options['no_annot'] == ''</filter>
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
47 </expand>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
48 <expand macro="annotation_orthologs_output_macro"/>
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
49 </outputs>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
50 <tests>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
51 <!-- test producing only seed orthologs-->
11
5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
galaxyp
parents: 10
diff changeset
52 <test expect_num_outputs="1">
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
53 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
54 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
55 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
56 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
57 <conditional name="annotation_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
58 <param name="no_annot" value="--no_annot"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
59 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
60 <section name="output_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
61 </section>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
62 <expand macro="seed_orthologs_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
63 <expand macro="stdout_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
64 </test>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
65
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
66 <!-- test producing annotations form seed orthologs -->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
67 <test expect_num_outputs="2">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
68 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
69 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
70 <param name="m" value="no_search"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
71 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
72 <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
73 </param>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
74 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
75 <conditional name="annotation_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
76 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
77 <section name="output_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
78 <param name="report_orthologs" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
79 </section>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
80 <expand macro="annotations_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
81 <expand macro="annotations_orthologs_assertion"/>
11
5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
galaxyp
parents: 10
diff changeset
82 <expand macro="stdout_assertion"/>
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
83 </test>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
84
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
85 <!-- test producing seed orthologs and annotations at once (ie the same as the previous two tests but in a single tool run) -->
11
5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
galaxyp
parents: 10
diff changeset
86 <test expect_num_outputs="3">
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
87 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
88 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
89 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
90 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
91 <section name="output_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
92 <param name="report_orthologs" value="true"/>
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
93 <param name="no_file_comments" value="false"/>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
94 <param name="md5" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
95 </section>
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
96 <expand macro="seed_orthologs_assertion" nocomments="false"/>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
97 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+" nocomments="false"/>
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
98 <expand macro="annotations_orthologs_assertion" nocomments="false"/>
11
5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
galaxyp
parents: 10
diff changeset
99 <expand macro="stdout_assertion"/>
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
100 </test>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
101
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
102 <!-- test using chached annotations from previous run -->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
103 <test expect_num_outputs="2">
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
104 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
105 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
106 <param name="m" value="cache"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
107 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
108 <param name="cache" value="DIA_nlim.emapper.annotations_cached" ftype="tabular"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
109 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
110 <section name="output_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
111 <param name="report_orthologs" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
112 <param name="md5" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
113 </section>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
114 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
115 <output name="no_annotations" ftype="fasta">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
116 <assert_contents>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
117 <has_n_lines n="0"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
118 </assert_contents>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
119 </output>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
120 <expand macro="stdout_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
121 </test>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
122
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
123 <!-- test setting tax scope-->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
124 <test expect_num_outputs="3">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
125 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
126 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
127 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
128 </conditional>
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
129 <section name="annotation_options">
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
130 <param name="tax_scope" value="651137" />
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
131 </section>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
132 <section name="output_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
133 <param name="report_orthologs" value="true"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
134 </section>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
135 <expand macro="seed_orthologs_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
136 <expand macro="annotations_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
137 <expand macro="annotations_orthologs_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
138 <expand macro="stdout_assertion">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
139 <has_text text="--tax_scope=651137"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
140 </expand>
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
141 </test>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
142
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
143 <!-- test setting a diamond option-->
11
5a30ae278db0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
galaxyp
parents: 10
diff changeset
144 <test expect_num_outputs="3">
8
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
145 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
146 <conditional name="ortho_method">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
147 <param name="m" value="diamond" />
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
148 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
149 <param name="sensmode" value="fast" />
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
150 </conditional>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
151 <section name="output_options">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
152 <param name="report_orthologs" value="true"/>
8
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
153 </section>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
154 <expand macro="seed_orthologs_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
155 <expand macro="annotations_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
156 <expand macro="annotations_orthologs_assertion"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
157 <expand macro="stdout_assertion">
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
158 <has_text text="--sensmode fast"/>
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
159 </expand>
8
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
160 </test>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
161 <!-- not enabled as it requires a specific .db file, hard to minimize -->
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
162 <!--test>
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
163 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
8
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
164 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
165 <section name="seed_ortho_options">
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
166 <conditional name="ortho_method">
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
167 <param name="m" value="mmseqs" />
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
168 <param name="start_sens" value="4" />
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
169 </conditional>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
170 </section>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
171 <param name="report_orthologs" value="true"/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
172 <param name="no_file_comments" value="true"/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
173 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
174 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
175 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
96cac424c870 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 7
diff changeset
176 </test-->
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
177 </tests>
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
178 <help><![CDATA[
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
179
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
180 eggnog-mapper
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
181 =============
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
182 Overview
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
183 --------
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
184
6
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
185 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
186 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
3cb37af59360 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
parents: 5
diff changeset
187 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
188 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
189
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
190 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
191
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
192 Outputs
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
193 -------
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
194
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
195 @HELP_SEARCH_OUTPUTS@
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
196
13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
197 @HELP_ANNOTATION_OUTPUTS@
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
198
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
galaxyp
parents: 12
diff changeset
199
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
200
12
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
201 **Recommentation for large input data**
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
202
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
203 EggNOG-mapper consists of two phases
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
204
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
205 1. finding seed orthologous sequences (compute intensive)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
206 2. expanding annotations (IO intensive)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
207
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
208 by default (i.e. if *Method to search seed orthologs* is not *Skip search stage...* and *Annotate seed orthologs* is *Yes*)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
209 both phases are executed within one tool run.
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
210
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
211 For large input FASTA datasets in can be favourable to split this in two separate
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
212 tool runs as follows:
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
213
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
214 1. Split the FASTA (e.g. 1M seqs per data set)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
215 2. Run the search phase only (set *Annotate seed orthologs* to *No*) on the separate FASTA files.
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
216 3. Run the annotation phase (set *Method to search seed orthologs* to *Skip search stage...*)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
217
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
218 See [also](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#Setting_up_large_annotation_jobs)
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
219
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
220 Another alternative is to use cached annotations (produced in a run with --md5 enabled).
9d1fbff733cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 11
diff changeset
221
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
222 ]]></help>
5
a5a3bdd0954b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
galaxyp
parents: 4
diff changeset
223 <expand macro="citations"/>
0
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
224 </tool>