Mercurial > repos > mikel-egana-aranguren > sparql_galaxy
annotate galaxy-dist/tools/sparql_galaxy/SPARQLGalaxy.xml @ 6:a579eb280308 draft default tip
Python script modified to render TSV results properly
author | mikel-egana-aranguren <mikel.egana.aranguren@gmail.com> |
---|---|
date | Fri, 07 Nov 2014 15:56:43 +0100 |
parents | 6501986529b0 |
children |
rev | line source |
---|---|
3
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
1 <tool id="SPARQLGalaxy" name="Execute an SPARQL query against an RDF file" version="1.0.1"> |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
2 <description>It executes an SPARQL query against the input RDF file and generates an HTML file with the variables and bound entities</description> |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
3 <command interpreter="python"> |
4
6501986529b0
HTML or tabular option added
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
3
diff
changeset
|
4 sparql.py $ontology "$pasted_query" $out_format > $output 2>/dev/null |
3
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
5 </command> |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
6 <inputs> |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
7 <param name="ontology" type="data" format="rdf" label="Input RDF file"/> |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
8 <param name="pasted_query" type="text" area="True" size="10x50" label="SPARQL Query" value="SELECT * WHERE { ?s ?p ?o }"> |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
9 <sanitizer sanitize="False"/> |
4
6501986529b0
HTML or tabular option added
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
3
diff
changeset
|
10 </param> |
6501986529b0
HTML or tabular option added
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
3
diff
changeset
|
11 <param name="out_format" type="select" label="Output format" help=""> |
6501986529b0
HTML or tabular option added
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
3
diff
changeset
|
12 <option value="html" selected="true">HTML</option> |
6501986529b0
HTML or tabular option added
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
3
diff
changeset
|
13 <option value="tab">TABULAR</option> |
3
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
14 </param> |
4
6501986529b0
HTML or tabular option added
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
3
diff
changeset
|
15 |
3
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
16 </inputs> |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
17 <outputs> |
4
6501986529b0
HTML or tabular option added
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
3
diff
changeset
|
18 <data format="html" name="output"> |
6501986529b0
HTML or tabular option added
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
3
diff
changeset
|
19 <change_format> |
6501986529b0
HTML or tabular option added
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
3
diff
changeset
|
20 <when input="out_format" value="tab" format="tabular" /> |
6501986529b0
HTML or tabular option added
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
3
diff
changeset
|
21 </change_format> |
6501986529b0
HTML or tabular option added
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
3
diff
changeset
|
22 </data> |
3
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
23 </outputs> |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
24 <help> |
4
6501986529b0
HTML or tabular option added
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
3
diff
changeset
|
25 |
3
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
26 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
27 **Important note** |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
28 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
29 RDFLib must be installed on the system (http://github.com/RDFLib/rdflib). |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
30 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
31 **Usage** |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
32 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
33 An RDF file (in any format that RDFLib can accept) and a SPARQL query are needed. See bundle for examples. |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
34 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
35 **More information** |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
36 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
37 Galaxy public instance with SPARQL-Galaxy pre-installed: |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
38 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
39 http://biordf.org:8983/ |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
40 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
41 RDF: |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
42 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
43 http://www.w3.org/standards/techs/rdf |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
44 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
45 SPARQL: |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
46 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
47 http://www.w3.org/standards/techs/sparql |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
48 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
49 **Contact** |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
50 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
51 Please send any request or comment to mikel.egana.aranguren@gmail.com. |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
52 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
53 </help> |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
54 |
24ad2706526c
Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents:
diff
changeset
|
55 </tool> |