Mercurial > repos > iuc > kobas

comparison kobas_macros.xml @ 0:720b1beabad6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 5dd86ae785ae71f697aab8ede735f394b39ad7bc-dirty
author iuc
date Sat, 05 Nov 2016 09:20:51 -0400
parents
children 83b998fa34ea
comparison
equal deleted inserted replaced
-1:000000000000 0:720b1beabad6
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>