Mercurial > repos > iuc > kobas
view kobas_macros.xml @ 3:83b998fa34ea draft
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author | iuc |
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date | Thu, 10 Nov 2016 16:21:41 -0500 |
parents | 720b1beabad6 |
children | 20f1b45dea63 |
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<macros> <token name="@WRAPPER_VERSION@">0.4</token> <token name="@KOBAS_VERSION@">2.1.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@KOBAS_VERSION@">kobas</requirement> </requirements> </xml> <xml name="input_kobasdb"> <param name="species" type="text" label="Species abbreviation" argument="--species" help="For example: ko for KEGG Orthology, hsa for Homo sapiens, mmu for Mus musculus, dme for Drosophila melanogaster, ath for Arabidopsis thaliana, sce for Saccharomyces cerevisiae and eco for Escherichia coli K-12 MG1655"/> <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"/> </xml> <xml name="blastdb_selector"> <param name="choice" type="select" label="BLAST Protein database"> <option value="histdb">BLAST database from your history</option> <option value="fasta">BLAST database from FASTA File</option> <option value="local" selected="True">Locally installed BLAST database</option> </param> <when value="fasta"> <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."/> <param name="histdb" type="hidden" value=""/> <param name="fasta" type="hidden" value=""/> </when> <when value="histdb"> <param name="localdb" type="hidden" value=""/> <param name="fastadb" type="hidden" value=""/> <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" 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"/> </when> <when value="local"> <param name="localdb" type="select" label="Protein BLAST database"> <options from_data_table="blastdb_p"/> </param> <param name="histdb" type="hidden" value=""/> <param name="fastadb" type="hidden" value=""/> </when> </xml> <xml name="kobas_citations"> <citations> <citation type="doi">10.1093/nar/gkr483</citation> </citations> </xml> <token name="@HELP_KOBAS_INFO@"> **KOBAS** 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 </token> <token name="@HELP_KOBAS_URL@"> KOBAS can be accessed at http://kobas.cbi.pku.edu.cn </token> </macros>