annotate monarch-homologues.xml @ 9:5fa1f0ca69cc draft default tip

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author nathandunn
date Sun, 25 Sep 2016 21:59:32 -0400
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1 <tool id="monarch-homologues" name="Pull Homologue Information from Monarch" version="0.1.0">
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2 <requirements/>
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3 <stdio>
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4 <exit_code range="1:" />
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5 </stdio>
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6 <command><![CDATA[
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7 #set conditional = "%20" + str($conditional1) + "%20"
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8 #set prefix = "subject_closure:%22"
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9 #set suffix = "%22"
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10 #set inputString = ""
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11 #for inputFile in $input1
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12 #set inputs = open(str($inputFile),'r').read().split(",")
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13 #for input in $inputs
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14 #if $inputString != ""
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15 #set inputString = $inputString + $conditional
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16 #end if
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17 #set inputString = $inputString + $prefix + str($input).strip(' \t\n\r') + $suffix
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18 #end for
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19 #end for
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20
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21 curl -s 'https://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=object,object_label,object_taxon,object_taxon_label,relation,relation_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=object_category:%22gene%22&fq=relation_closure:%22RO:HOM0000001%22&facet.field=subject_taxon_closure_label&facet.field=object_taxon_closure_label&q=*:*' | tail -n +2 > $output1
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22 ]]></command>
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23 <inputs>
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24 <param name="input1" type="data" format="tabular" multiple="true" label="Gene" />
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25 <param name="conditional1" type="select" multiple="false" display="radio" label="Conditional">
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26 <option value="AND">and</option>
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27 <option value="OR">or</option>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data name="output1" type="data" format="tabular" />
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input1" value="gene.tsv"/>
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36 <param name="conditional1" value="OR"/>
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37 <output name="output1" file="homologues-for-gene.tsv"/>
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38 </test>
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39 <test>
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40 <param name="input1" value="2-genes.tsv"/>
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41 <param name="conditional1" value="OR"/>
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42 <output name="output1" file="homologues-for-genes-union.tsv"/>
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43 </test>
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44 <test>
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45 <param name="input1" value="2-genes.tsv"/>
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46 <param name="conditional1" value="AND"/>
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47 <output name="output1" file="homologues-for-genes-intersection.tsv"/>
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48 </test>
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49 </tests>
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50 <help><![CDATA[
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51 Pulls data from monarch web services as TSV given a gene.
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52 object,object_label,object_taxon,object_taxon_label,relation,relation_label,evidence,evidence_label,source,is_defined_by,qualifier
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53 ]]></help>
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54 <citations>
1
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55 <citation type="doi">doi:10.5281/zenodo.56412</citation>
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56 </citations>
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57 </tool>