Mercurial > repos > iuc > kobas
comparison kobas_macros.xml @ 0:720b1beabad6 draft
planemo upload commit 5dd86ae785ae71f697aab8ede735f394b39ad7bc-dirty
author | iuc |
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date | Sat, 05 Nov 2016 09:20:51 -0400 |
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children | 83b998fa34ea |
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-1:000000000000 | 0:720b1beabad6 |
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1 <macros> | |
2 <token name="@WRAPPER_VERSION@">0.3</token> | |
3 <token name="@KOBAS_VERSION@">2.1.1</token> | |
4 <xml name="input_kobasdb"> | |
5 <param | |
6 name="species" | |
7 type="text" | |
8 label="Species abbreviation" | |
9 argument="--species" | |
10 help="For example: ko for KEGG | |
11 Orthology, hsa for Homo sapiens, mmu for Mus musculus, | |
12 dme for Drosophila melanogaster, ath for Arabidopsis | |
13 thaliana, sce for Saccharomyces cerevisiae and eco for | |
14 Escherichia coli K-12 MG1655"/> | |
15 <param format="sqlite" name="kobasdb" type="data" label="KOBAS database" help="KOBAS species database, available for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/> | |
16 </xml> | |
17 <xml name="blastdb_selector"> | |
18 <param name="choice" type="select" label="BLAST Protein database"> | |
19 <option value="histdb">BLAST database from your history</option> | |
20 <option value="fasta">BLAST database from FASTA File</option> | |
21 <option value="local" selected="True">Locally installed BLAST database</option> | |
22 </param> | |
23 <when value="fasta"> | |
24 <param name="fastadb" format="fasta" type="data" label="FASTA File for BLAST DB" help="FASTA file which will be used to create a BLAST database with makeblastdb."/> | |
25 <param name="histdb" type="hidden" value=""/> | |
26 <param name="fasta" type="hidden" value=""/> | |
27 </when> | |
28 <when value="histdb"> | |
29 <param name="localdb" type="hidden" value=""/> | |
30 <param name="fastadb" type="hidden" value=""/> | |
31 <param | |
32 name="histdb" | |
33 type="data" | |
34 format="blastdbp" | |
35 label="Protein BLAST database" | |
36 help="The protein BlAST database used by KOBAS. FASTA files to create BLAST databases with makeblastdb can be found for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/> | |
37 </when> | |
38 <when value="local"> | |
39 <param name="localdb" type="select" label="Protein BLAST database"> | |
40 <options from_data_table="blastdb_p"/> | |
41 </param> | |
42 <param name="histdb" type="hidden" value=""/> | |
43 <param name="fastadb" type="hidden" value=""/> | |
44 </when> | |
45 </xml> | |
46 <xml name="kobas_citations"> | |
47 <citations> | |
48 <citation type="doi">10.1093/nar/gkr483</citation> | |
49 </citations> | |
50 </xml> | |
51 | |
52 <token name="@HELP_KOBAS_INFO@"> | |
53 **KOBAS** | |
54 | |
55 KOBAS is a KEGG Orthology Based Annotation System. Its purpose is to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases. The necessary KOBAS databases for multiple species can be downloaded from http://kobas.cbi.pku.edu.cn/download.php | |
56 </token> | |
57 <token name="@HELP_KOBAS_URL@"> | |
58 KOBAS can be accessed at http://kobas.cbi.pku.edu.cn | |
59 </token> | |
60 </macros> |