annotate bioentityset-overrepresentation.xml @ 5:6eaaeedf2f37 draft default tip

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1 <tool id="monarch-bioentityset-overrepresentation" name="Bioentity Set Get Over Representation" version="0.1.0">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <requirements>
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6 <requirement type="package" version="1.5">jq</requirement>
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7 </requirements>
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8 <expand macro="frontmatter" />
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9 <command><![CDATA[
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10 #*
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11 curl --silent -X GET --header 'Accept: application/json' 'https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/?object_category=phenotype&subject=NCBIGene%3A6295&subject=NCBIGene%3A1258&subject=NCBIGene%3A3614&subject=NCBIGene%3A26121&subject=NCBIGene%3A7275&subject=NCBIGene%3A55857&subject=NCBIGene%3A79797&subject=NCBIGene%3A10594&subject=NCBIGene%3A64218&subject=NCBIGene%3A7401&ontology=hp&subject_category=gene&taxon=NCBITaxon%3A9606&object_category=phenotype&max_p_value=0.05' > $output
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12 *#
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13 #set $subject_string = ''
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14 #set $subject = $subject.replace(' ', '')
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15 #set $subject = $subject.replace(',', ' ')
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16 #for $word in $subject.split(' ')
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17 #set $subject_string += '&subject='+str($word)
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18 #end for
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19
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20 #set $background_string = ''
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21 #set $background = $background.replace(' ', '')
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22 #set $background = $background.replace(',', ' ')
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23 #for $word in $background.split(' ')
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24 #set $background_string += '&background='+str($word)
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25 #end for
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26
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27 curl --silent -X GET --header 'Accept: application/json' 'https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/?object_category=$object_category$subject_string&background=$background_string&ontology=$ontology&subject_category=$subject_category&taxon=$taxon&object_category=$object_category&max_p_value=$max_p_value' > $output_json
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28
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29 &&
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30
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31 echo -e "p\tn\tp_uncorrected\tc" > $output_tsv
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32
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33 &&
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34
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35 cat $output_json | jq -r '.results[] | flatten | @tsv ' >> $output_tsv
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36 ]]></command>
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37 <inputs>
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38 <param name="object_category" type="text" format="txt" multiple="false" label="CATEGORY of entity at link OBJECT (target), e.g. function, phenotype, disease" />
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39 <param name="subject" type="text" format="txt" multiple="true" label="Entity ids to be examined, e.g. NCBIGene:6295,NCBIGene:1258 ,NCBIGene:3614 ,NCBIGene:26121 ,NCBIGene:7275 ,NCBIGene:55857 ,NCBIGene:79797 ,NCBIGene:10594 ,NCBIGene:64218 ,NCBIGene:7401"
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40 />
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41 <param name="background" type="text" format="txt" multiple="true" label="Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests" />
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42 <param name="ontology" type="text" format="txt" multiple="false" value="hp" label="ontology id. Must be obo id. Examples: go, mp, hp, uberon (optional: will be inferred if left blank)" />
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43 <param name="subject_category" type="text" format="txt" multiple="false" label="Other types may be used e.g. disease but statistics may not make sense" value="gene"/>
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44 <param name="taxon" type="text" format="txt" multiple="true" label="must be NCBITaxon CURIE. Example: NCBITaxon:9606" />
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45 <param name="object_category" type="text" format="txt" multiple="false" label="E.g. phenotype, function" value="phenotype" />
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46 <param name="max_p_value" type="text" format="txt" multiple="false" value="0.05" label="Exclude results with p-value greater than this"/>
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47 </inputs>
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48 <outputs>
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49 <data name="output_json" format="json"/>
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50 <data
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51 name="output_tsv"
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52 format="tsv"
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53 >
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54 </data>
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55 </outputs>
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56 <tests>
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57 <!--
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58
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59 emulate: https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/
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60 ?object_category=phenotype
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61 subject=NCBIGene%3A6295
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62 subject=NCBIGene%3A1258
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63 subject=NCBIGene%3A3614
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64 subject=NCBIGene%3A26121
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65 subject=NCBIGene%3A7275
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66 subject=NCBIGene%3A55857
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67 subject=NCBIGene%3A79797
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68 subject=NCBIGene%3A10594
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69 subject=NCBIGene%3A64218
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70 subject=NCBIGene%3A7401
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71 ontology=hp
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72 subject_category=gene
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73 taxon=NCBITaxon%3A9606
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74 object_category=phenotype
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75 max_p_value=0.05-->
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76 <test>
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77 <param name="object_category" value="phenotype"/>
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78 <param name="subject" value="NCBIGene%3A6295,NCBIGene%3A1258,NCBIGene%3A3614,NCBIGene%3A26121,NCBIGene%3A7275,NCBIGene%3A55857,NCBIGene%3A79797,NCBIGene%3A10594,NCBIGene%3A64218,NCBIGene%3A7401"/>
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79 <param name="ontology" value="hp"/>
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80 <param name="subject_category" value="gene"/>
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81 <param name="taxon" value="NCBITaxon:9606"/>
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82 <param name="object_category" value="phenotype"/>
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83 <param name="max_p_value" value="0.05"/>
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84 <output name="output_json" file="bioentityset-overrepresentation.json"/>
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85 <output name="output_tsv" file="bioentityset-overrepresentation.tsv"/>
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86 </test>
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87 </tests>
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88 <expand macro="citations" />
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89 </tool>
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90