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annotate matrix.xml @ 35:fa736576c7ed draft

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author jjkoehorst
date Mon, 04 Jul 2016 10:37:59 -0400
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1 <tool id="DMatrix" name="MATSPARQL" version="1.0.1">
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2 <description/>
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3 <requirements>
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4 <container type="docker">jjkoehorst/sappdocker:MATRIX</container>
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5 </requirements>
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6 <command interpreter="docker">java -jar /sparql/sparqljava-0.0.1-SNAPSHOT-jar-with-dependencies.jar '$separate' '-rdf' '$input' '-format' 'TURTLE' '-query' '$query' '-output' '$output' &amp;&amp; Rscript $__tool_directory__/matrix.R '$output' '$output' </command>
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7 <inputs>
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8 <param format="ttl" label="Genome Database" multiple="True" name="input" type="data"/>
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9 <param area="True" label="SPARQL query" name="query" type="text" value="YOUR QUERY HERE"/>
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10 <param checked="False" falsevalue="" help="Use this option if you run into memory or performance problems. Each genome will be queried independently of each other and therefor advanced comparison SPARQL queries will not work" label="Treath genomes separately" name="separate" truevalue="-separate" type="boolean"/>
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11 </inputs>
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12 <outputs>
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13 <data format="tsv" label="matrix.tsv" name="output"/>
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14 </outputs>
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15 <help>The creation of a matrix from a created SPARQL query. One should use a query that creates 3 columns for the X and Y coordinates and Z for the value.
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16
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17 A header for a SPARQL query would look like SELECT ?genome ?protein ?value or SELECT ?genome ?domain (COUNT(?domain) AS ?domainC)
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18
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19 -----------------------------
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20 Genome Interpro Matrix
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21 -----------------------------
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22 The following query results in a matrix of genomes by Pfam accessions ::
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23
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24 PREFIX biopax:&lt;http://www.biopax.org/release/bp-level3.owl#&gt;
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25 PREFIX ssb:&lt;http://csb.wur.nl/genome/&gt;
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26 SELECT DISTINCT ?genome ?id (COUNT(?id) AS ?value)
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27 WHERE {
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28 ?genome a ssb:Genome .
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29 ?genome ssb:dnaobject ?dna .
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30 ?dna ssb:feature ?feature .
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31 ?feature ssb:tool ?tool .
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32 ?feature ssb:protein ?protein .
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33 ?protein ssb:feature ?domain .
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34 ?domain ssb:signature ?signature .
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35 ?signature biopax:xref ?xref .
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36 ?xref biopax:db 'pfam' .
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37 ?xref biopax:id ?id .
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38 } GROUP BY ?genome ?id
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39
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40 -------------------
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41 Enzyme based matrix
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42 -------------------
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43
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44 The following query results in a matrix of genomes by EC numbers ::
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45
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46 PREFIX ssb:&lt;http://csb.wur.nl/genome/&gt;
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47 SELECT ?genome ?ec (COUNT(?ec) AS ?ecCount)
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48 WHERE {
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49 ?gene a ssb:Cds .
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50 ?gene ssb:locus_tag ?locus .
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51 ?gene ssb:source ?source .
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52 ?gene ssb:protein ?protein .
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53 ?protein ssb:feature ?feature .
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54 {
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55 ?feature ssb:kegg ?ec .
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56 } UNION {
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57 ?feature ssb:ec_number ?ec .
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58 }
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59 } GROUP BY ?genome ?ec
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60
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61 **If you require specific questions related to the database that you created feel free to contact us.**
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62 </help>
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63 </tool>