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1 <tool name="CEAS: build database" id="ceas_build_db" version="0.1.0">
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2 <description>with gene annotation and genome background</description>
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3 <macros>
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4 <import>ceas_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command interpreter="command">
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8 build_genomeBG
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9 #if $ref.refsrc == 'ucsc':
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10 -d $ref.dbkey -g $ref.gene_table
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11 #elif $ref.refsrc == 'history':
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12 -g $ref.gdb
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13 #elif $ref.refsrc == 'cached':
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14 -g $ref.ceas_db
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15 #end if
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16 -w $wfile -o $output
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17 </command>
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18 <inputs>
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19 <conditional name="ref">
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20 <param name="refsrc" type="select" label="">
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21 <option value="ucsc">From UCSC</option>
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22 <option value="history">From history</option>
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23 <option value="cached">Locally cached CEAS db</option>
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24 </param>
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25 <when value="ucsc">
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26 <param name="dbkey" type="text" value="" label="A UCSC genome id, e.g. mm9">
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27 </param>
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28 <param name="gene_table" type="text" value="" label="A UCSC gene table name, e.g. refGene">
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29 </param>
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30 </when>
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31 <when value="cached">
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32 <param name="ceas_db" type="select" label="">
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33 <options from_data_table="ceasdb">
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34 <filter type="unique_value" column="0" />
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35 </options>
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36 </param>
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37 </when>
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38 <when value="history">
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39 <param name="gdb" type="data" format="ceasdb" label="Gene annotation table file (sqlite3)">
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40 </param>
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41 </when>
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42 </conditional>
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43 <param name="wfile" type="data" format="wig,bigwig" label="wig / bigwig file">
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44 <!-- <validator type="unspecified_build" /> -->
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45 </param>
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46 </inputs>
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47 <outputs>
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48 <data format="ceasdb" name="output" label=""/>
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49 </outputs>
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50 <tests>
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51 </tests>
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52 <help>
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53 ** CEAS **
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54 This tool annotates the given intervals and scores with genome
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55 features such as gene body. It's the major module in CEAS package
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56 which is written by Hyunjin Gene Shin, published in Bioinformatics
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57 (pubmed id:19689956).
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58
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59 @EXTERNAL_DOCUMENTATION@
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60
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61 @CITATION_SECTION@
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62
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63 </help>
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64
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65 </tool>
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