Mercurial > repos > nathandunn > monarchinitiative
annotate monarch-phenopackets.xml @ 4:4be31c7908af draft
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author | nathandunn |
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date | Mon, 27 Jun 2016 09:48:53 -0400 |
parents | 7ae426ca9054 |
children | 7648db7c7168 |
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1 <tool id="monarch-phenotypes-for-disease" name="Pull Diseases from Phenotypes" 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') + $suffix |
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18 #end for |
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19 #end for |
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20 |
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21 curl -s 'https://monarchinitiative.org/phenopacket?q=*:*&fq=($inputString)&sfq=subject_category:%22variant%22&personality=variant_phenotype' > $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="Variant"/> |
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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="json"/> |
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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="phenotype.tsv"/> |
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36 <param name="conditional1" value="OR"/> |
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37 <!--<output name="output1" file="phenotypes-for-variant.json"/>--> |
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38 <output name="output1"> |
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39 <assert_contents> |
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40 <has_text text='phenopacket":{"phenotype_profile":[{"entity":"ClinVarVariant:217207"'/> |
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41 </assert_contents> |
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42 </output> |
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43 </test> |
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44 <test> |
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45 <param name="input1" value="2-phenotypes.tsv"/> |
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46 <param name="conditional1" value="AND"/> |
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47 <!--<output name="output1" file="phenotypes-for-variants-intersection.json"/>--> |
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48 <output name="output1"> |
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49 <assert_contents> |
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50 <has_text text='phenopacket":{"phenotype_profile":[{"entity":"ClinVarVariant:217207"'/> |
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51 </assert_contents> |
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52 </output> |
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53 </test> |
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54 <test> |
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55 <param name="input1" value="2-phenotypes.tsv"/> |
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56 <param name="conditional1" value="OR"/> |
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57 <!--<output name="output1" file="phenotypes-for-variants-union.json"/>--> |
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58 <output name="output1"> |
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59 <assert_contents> |
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60 <has_text text='phenopacket":{"phenotype_profile":[{"entity":"ClinVarVariant:217207"'/> |
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61 </assert_contents> |
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62 </output> |
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63 </test> |
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64 </tests> |
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65 <help><![CDATA[ |
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66 Pulls phenopacket from data from monarch web services from one or more variants. |
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67 https://github.com/phenopackets/phenopacket-format/wiki/Getting-Started |
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68 ]]></help> |
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69 <citations> |
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70 <citation type="doi">doi:10.5281/zenodo.56412</citation> |
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71 </citations> |
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72 </tool> |