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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kobas commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 09:14:20 +0000
parents d1f8912a4796
children
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1 <macros>
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2 <token name="@TOOL_VERSION@">2.1.1</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">kobas</requirement>
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6 <!-- kobas 2.1.1 is not compatible with Biopython >=1.73 due to https://github.com/biopython/biopython/issues/1952 -->
d1f8912a4796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kobas commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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7 <requirement type="package" version="1.72">biopython</requirement>
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8 <!-- Help conda resolving the enviroment, hopefully this can be removed for next update -->
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9 <requirement type="package" version="3.4">r-base</requirement>
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10 </requirements>
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11 </xml>
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12 <xml name="input_kobasdb">
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13 <param argument="--species" type="text" label="Species abbreviation"
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14 help="For example: ko for KEGG Orthology, hsa for Homo sapiens, mmu
d1f8912a4796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kobas commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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15 for Mus musculus, dme for Drosophila melanogaster, ath for
d1f8912a4796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kobas commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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16 Arabidopsis thaliana, sce for Saccharomyces cerevisiae and eco
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17 for Escherichia coli K-12 MG1655"/>
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18 <param name="kobasdb" type="data" format="sqlite" label="KOBAS database" help="KOBAS species database, available for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/>
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19 </xml>
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20 <xml name="blastdb_selector">
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21 <param name="choice" type="select" label="BLAST Protein database">
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22 <option value="histdb">BLAST database from your history</option>
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23 <option value="fasta">BLAST database from FASTA File</option>
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24 <option value="local" selected="True">Locally installed BLAST database</option>
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25 </param>
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26 <when value="fasta">
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27 <param name="fastadb" type="data" format="fasta" label="FASTA File for BLAST DB" help="FASTA file which will be used to create a BLAST database with makeblastdb."/>
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28 </when>
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29 <when value="histdb">
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30 <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database"
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31 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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32 </when>
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33 <when value="local">
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34 <param name="localdb" type="select" label="Protein BLAST database">
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35 <options from_data_table="blastdb_p"/>
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36 </param>
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37 </when>
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38 </xml>
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39 <xml name="kobas_citations">
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40 <citations>
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41 <citation type="doi">10.1093/nar/gkr483</citation>
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42 </citations>
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43 </xml>
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44
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45 <token name="@HELP_KOBAS_INFO@">
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46 **KOBAS**
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47
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48 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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49 </token>
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50 <token name="@HELP_KOBAS_URL@">
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51 KOBAS can be accessed at http://kobas.cbi.pku.edu.cn
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52 </token>
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53 </macros>