Mercurial > repos > nathandunn > biolinkmonarchinitiative

comparison bioentityset-overrepresentation.xml @ 4:49b46f044d48 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 0dbcda86caba8f8fead7cb6fde0ae3e73d398f1e
author nathandunn
date Mon, 04 Dec 2017 19:35:12 -0500
parents d40860663861
children 6eaaeedf2f37
comparison
equal deleted inserted replaced
3:d40860663861 4:49b46f044d48
19 #set $background = $background.replace(',', ' ') 19 #set $background = $background.replace(',', ' ')
20 #for $word in $background.split(' ') 20 #for $word in $background.split(' ')
21 #set $background_string += '&background='+str($word) 21 #set $background_string += '&background='+str($word)
22 #end for 22 #end for
23 23
24 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' > $output 24 curl --silent -X GET --header 'Accept: application/json' 'https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/?object_category=$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
25
26 &&
27
28 echo -e "p\tn\tp_uncorrected\tc" > $output_tsv
29
30 &&
31
32 cat $output_json | jq -r '.results[] | flatten | @tsv ' >> $output_tsv
25 ]]></command> 33 ]]></command>
26 <inputs> 34 <inputs>
27 <param name="object_category" type="text" format="txt" multiple="false" label="CATEGORY of entity at link OBJECT (target), e.g. function, phenotype, disease" /> 35 <param name="object_category" type="text" format="txt" multiple="false" label="CATEGORY of entity at link OBJECT (target), e.g. function, phenotype, disease" />
28 <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" 36 <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"
29 /> 37 />
32 <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"/> 40 <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"/>
33 <param name="taxon" type="text" format="txt" multiple="true" label="must be NCBITaxon CURIE. Example: NCBITaxon:9606" /> 41 <param name="taxon" type="text" format="txt" multiple="true" label="must be NCBITaxon CURIE. Example: NCBITaxon:9606" />
34 <param name="object_category" type="text" format="txt" multiple="false" label="E.g. phenotype, function" value="phenotype" /> 42 <param name="object_category" type="text" format="txt" multiple="false" label="E.g. phenotype, function" value="phenotype" />
35 <param name="max_p_value" type="text" format="txt" multiple="false" value="0.05" label="Exclude results with p-value greater than this"/> 43 <param name="max_p_value" type="text" format="txt" multiple="false" value="0.05" label="Exclude results with p-value greater than this"/>
36 </inputs> 44 </inputs>
37 <expand macro="outputs" /> 45 <outputs>
46 <data name="output_json" format="json"/>
47 <data
48 name="output_tsv"
49 format="tsv"
50 header_row="1"
51 >
52 </data>
53 </outputs>
38 <tests> 54 <tests>
39 <!--emulate: https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/ 55 <!--
56
57 emulate: https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/
40 ?object_category=phenotype 58 ?object_category=phenotype
41 subject=NCBIGene%3A6295 59 subject=NCBIGene%3A6295
42 subject=NCBIGene%3A1258 60 subject=NCBIGene%3A1258
43 subject=NCBIGene%3A3614 61 subject=NCBIGene%3A3614
44 subject=NCBIGene%3A26121 62 subject=NCBIGene%3A26121
59 <param name="ontology" value="hp"/> 77 <param name="ontology" value="hp"/>
60 <param name="subject_category" value="gene"/> 78 <param name="subject_category" value="gene"/>
61 <param name="taxon" value="NCBITaxon:9606"/> 79 <param name="taxon" value="NCBITaxon:9606"/>
62 <param name="object_category" value="phenotype"/> 80 <param name="object_category" value="phenotype"/>
63 <param name="max_p_value" value="0.05"/> 81 <param name="max_p_value" value="0.05"/>
64 <output name="output" file="bioentityset-overrepresentation.json"/> 82 <output name="output_json" file="bioentityset-overrepresentation.json"/>
83 <output name="output_tsv" file="bioentityset-overrepresentation.tsv"/>
65 </test> 84 </test>
66 </tests> 85 </tests>
67 <expand macro="citations" /> 86 <expand macro="citations" />
68 </tool> 87 </tool>
69 88