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annotate kobas_macros.xml @ 0:720b1beabad6 draft

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author iuc
date Sat, 05 Nov 2016 09:20:51 -0400
parents
children 83b998fa34ea
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1 <macros>
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2 <token name="@WRAPPER_VERSION@">0.3</token>
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3 <token name="@KOBAS_VERSION@">2.1.1</token>
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4 <xml name="input_kobasdb">
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5 <param
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6 name="species"
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7 type="text"
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8 label="Species abbreviation"
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9 argument="--species"
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10 help="For example: ko for KEGG
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11 Orthology, hsa for Homo sapiens, mmu for Mus musculus,
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12 dme for Drosophila melanogaster, ath for Arabidopsis
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13 thaliana, sce for Saccharomyces cerevisiae and eco for
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14 Escherichia coli K-12 MG1655"/>
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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"/>
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16 </xml>
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17 <xml name="blastdb_selector">
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18 <param name="choice" type="select" label="BLAST Protein database">
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19 <option value="histdb">BLAST database from your history</option>
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20 <option value="fasta">BLAST database from FASTA File</option>
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21 <option value="local" selected="True">Locally installed BLAST database</option>
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22 </param>
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23 <when value="fasta">
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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."/>
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25 <param name="histdb" type="hidden" value=""/>
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26 <param name="fasta" type="hidden" value=""/>
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27 </when>
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28 <when value="histdb">
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29 <param name="localdb" type="hidden" value=""/>
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30 <param name="fastadb" type="hidden" value=""/>
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31 <param
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32 name="histdb"
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33 type="data"
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34 format="blastdbp"
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35 label="Protein BLAST database"
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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"/>
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37 </when>
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38 <when value="local">
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39 <param name="localdb" type="select" label="Protein BLAST database">
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40 <options from_data_table="blastdb_p"/>
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41 </param>
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42 <param name="histdb" type="hidden" value=""/>
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43 <param name="fastadb" type="hidden" value=""/>
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44 </when>
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45 </xml>
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46 <xml name="kobas_citations">
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47 <citations>
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48 <citation type="doi">10.1093/nar/gkr483</citation>
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49 </citations>
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50 </xml>
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51
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52 <token name="@HELP_KOBAS_INFO@">
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53 **KOBAS**
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54
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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
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56 </token>
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57 <token name="@HELP_KOBAS_URL@">
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58 KOBAS can be accessed at http://kobas.cbi.pku.edu.cn
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59 </token>
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60 </macros>