Mercurial > repos > mikel-egana-aranguren > sadi_docker
changeset 0:54c48f9ca32b default tip
first release
| author | Mikel Egana <mikel.egana.aranguren@gmail.com> |
|---|---|
| date | Fri, 04 Sep 2015 23:24:45 +0200 |
| parents | |
| children | |
| files | tools/SADI-Docker/SADI-Docker-RDFSyntaxConverter.xml tools/SADI-Docker/SADI-Docker-SPARQLGalaxy.xml tools/SADI-Docker/SADI-Docker-mergeRDFgraphs.xml tools/SADI-Docker/SADI-Docker-rapper.xml tools/SADI-Docker/SADI-Docker-sadi_client.xml tools/SADI-Docker/SADI-Docker-tab2rdf.xml |
| diffstat | 6 files changed, 271 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/SADI-Docker/SADI-Docker-RDFSyntaxConverter.xml Fri Sep 04 23:24:45 2015 +0200 @@ -0,0 +1,49 @@ +<tool id="SADI-Docker-RDFSyntaxConverter" name="SADI - RDF Syntax Converter" version="0.1"> + <description>Converts RDF to N3, N-TRIPLE or TAB format</description> + <requirements> + <container type="docker">mikeleganaaranguren/sadi:v6</container> + </requirements> + + <command>java -jar sadi/RDFSyntaxConverter.jar $input $format > $output 2>/dev/null</command> + + <inputs> + <param name="input" type="data" format="rdf" label="RDF input file"/> + <param name="format" type="select" label="Choose RDF output format"> + <option value="N3">N3</option> + <option value="N-TRIPLE">N-TRIPLE</option> + <option value="TAB" selected="true">Tab separated columns</option> + </param> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="hello-input.rdf"/> + <param name="format" value="N3"/> + <output name="output" file="RDFSyntaxConverter_N3_test_hello_output"/> + </test> + <test> + <param name="input" value="hello-input.rdf"/> + <param name="format" value="N-TRIPLE"/> + <output name="output" file="RDFSyntaxConverter_N-TRIPLE_test_hello_output"/> + </test> + <test> + <param name="input" value="hello-input.rdf"/> + <param name="format" value="TAB"/> + <output name="output" file="RDFSyntaxConverter_TAB_test_hello_output"/> + </test> + </tests> + <help> + + **What it does** + + Given an RDF input file, it converts it to N3, N-TRIPLE or TAB (A tab delimited file containing three columns -subjects, predicates and objects- for other Galaxy tools to consume). + + **About** + + More information and contact: http://github.com/mikel-egana-aranguren/SADI-Docker-Galaxy. + + </help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/SADI-Docker/SADI-Docker-SPARQLGalaxy.xml Fri Sep 04 23:24:45 2015 +0200 @@ -0,0 +1,39 @@ +<tool id="SADI-Docker-SPARQLGalaxy" name="SADI - Execute an SPARQL query against an RDF file" version="0.1"> + <description>It executes an SPARQL query against the input RDF file and generates an HTML file with the variables and bound entities</description> + <requirements> + <container type="docker">mikeleganaaranguren/sadi:v6</container> + </requirements> + <command> + python /sadi/sparql.py $ontology "$pasted_query" $out_format > $output 2>/dev/null + </command> + <inputs> + <param name="ontology" type="data" format="rdf" label="Input RDF file"/> + <param name="pasted_query" type="text" area="True" size="10x50" label="SPARQL Query" value="SELECT * WHERE { ?s ?p ?o }"> + <sanitizer sanitize="False"/> + </param> + <param name="out_format" type="select" label="Output format" help=""> + <option value="html" selected="true">HTML</option> + <option value="tab">TABULAR</option> + </param> + + </inputs> + <outputs> + <data format="html" name="output"> + <change_format> + <when input="out_format" value="tab" format="tabular" /> + </change_format> + </data> + </outputs> + <help> + +**Usage** + + An RDF file (in any format that RDFLib can accept) and a SPARQL query are needed. + +**About** + + More information and contact: http://github.com/mikel-egana-aranguren/SADI-Docker-Galaxy. + + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/SADI-Docker/SADI-Docker-mergeRDFgraphs.xml Fri Sep 04 23:24:45 2015 +0200 @@ -0,0 +1,36 @@ +<tool id="SADI-Docker-mergeRDFgraphs" name="SADI - Merge RDF Graphs" version="0.1"> + <description>Merge RDF graphs</description> + <requirements> + <container type="docker">mikeleganaaranguren/sadi:v6</container> + </requirements> + <command> + python /sadi/MergeRDFGraphs.py + #for $i in $input_files + ${i.input_file} + #end for + > $output_file + </command> + <inputs> + <repeat name="input_files" title="Input RDF file"> + <param name="input_file" type="data" format="rdf" label="RDF file"/> + </repeat> + </inputs> + <outputs> + <data name="output_file" format="rdf"/> + </outputs> + <help> + +**What it does** + +Merge RDF graphs from history. + +**Output Format** + +Output RDF format is RDF/XML by default. + +**About** + +More information and contact: http://github.com/mikel-egana-aranguren/SADI-Docker-Galaxy. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/SADI-Docker/SADI-Docker-rapper.xml Fri Sep 04 23:24:45 2015 +0200 @@ -0,0 +1,32 @@ +<tool id="SADI-Docker-rapper" name="SADI - RDF Format (Rapper)" version="0.1"> + <description>RDF converter (Rapper)</description> + <requirements> + <container type="docker">mikeleganaaranguren/sadi:v6</container> + </requirements> + <command> + rapper -q $input_file -i $input_format -o $output_format > $output_file + </command> + <inputs> + <param name="input_file" type="data" label="Input File"/> + <param name="input_format" type="select" label="Input Format"> + <option value="ntriples">N-Triples</option> + <option value="turtle">Turtle</option> + <option value="rdfxml">RDF/XML</option> + </param> + <param name="output_format" type="select" label="Output Format"> + <option value="ntriples">N-Triples</option> + <option value="turtle">Turtle</option> + <option value="rdfxml">RDF/XML</option> + </param> + </inputs> + <outputs> + <data name="output_file" format="rdf" label="${tool.name} on ${on_string}"/> + </outputs> + <help> + +**What it does** + +This tool converts RDF format from/to N-Triples, Turtle, RDF/XML with Raptor's Rapper. + + </help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/SADI-Docker/SADI-Docker-sadi_client.xml Fri Sep 04 23:24:45 2015 +0200 @@ -0,0 +1,30 @@ +<tool id="SADI-Docker-sadi_client" name="SADI client" version="0.1"> + <description>Invoke a SADI service, given an input RDF, synchronously</description> + <requirements> + <container type="docker">mikeleganaaranguren/sadi:v6</container> + </requirements> + + <command>java -jar /sadi/sadi_client.jar $url $input > $output 2>/dev/null</command> + + <inputs> + <param name="url" type="text" size="250" label="Service URL"> + <sanitizer sanitize="False"/><!-- Disable sanitizer for URLs with e.g. tilde character --> + </param> + <param name="input" type="data" format="rdf" label="RDF input for SADI service"/> + </inputs> + <outputs> + <data format="rdf" name="output" /> + </outputs> + + <help> + + **What it does** + + Given an RDF input and a SADI service URL, sends the input to the service obtaining an output, synchronously. + + **About** + + More information and contact: http://github.com/mikel-egana-aranguren/SADI-Docker-Galaxy. + + </help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/SADI-Docker/SADI-Docker-tab2rdf.xml Fri Sep 04 23:24:45 2015 +0200 @@ -0,0 +1,85 @@ +<tool id="SADI-Docker-tab2rdf" name="SADI - Tab-to-RDF" version="0.1"> + + <!-- Modified by Mikel Egaña Aranguren, very hacky --> + + <description>Converter</description> + + <requirements> + <container type="docker">mikeleganaaranguren/sadi:v6</container> + </requirements> + <command> + #if $namespace.choose_namespace=="none" + python /sadi/tab2rdf.py $input_file $output_file $output_format none + #for $i in $triples + ${i.s_col} ${i.p_val} ${i.o_col} ${i.o_type} + #end for + #else + python /sadi/tab2rdf.py $input_file $output_file $output_format $namespace.choosen_namespace + #for $i in $triples + ${i.s_col} ${i.p_val} ${i.o_col} ${i.o_type} + #end for + #end if + </command> + <inputs> + <param name="input_file" type="data" format="tabular" label="Input File (tabular)"/> + + <conditional name="namespace"> + <param name="choose_namespace" type="select" label="Add namespace?"> + <option value="none">No (The tab file includes complete URIs for each resource)</option> + <option value="yes_choose_namespace">Yes</option> + </param> + <when value="yes_choose_namespace"> + <param name="choosen_namespace" type="text" size="50" value="http://localhost/" label="Namespace" /> + </when> + </conditional> + + <param name="output_format" type="select" label="Output Format"> + <option value="ntriples">N-Triples</option> + <option value="turtle">Turtle</option> + <option value="rdfxml">RDF/XML</option> + </param> + <repeat name="triples" title="Triples"> + <param name="s_col" type="data_column" data_ref="input_file" label="Subject (column)" /> + <param name="p_val" type="text" size="50" value="a" label="Predicate (text)"> + <sanitizer sanitize="False"/> + </param> + <param name="o_col" type="data_column" data_ref="input_file" label="Object (column)" /> + <param name="o_type" label="Check if this object is Literal (Keep unchecked if this object is URI)" type="boolean" truevalue="1" falsevalue="0" checked="False"/> + </repeat> + </inputs> + <outputs> + <data name="output_file" format="rdf" label="${tool.name} on ${on_string}"/> + </outputs> + <help> + +**Important note** + +This is a modified version of Tab2RDF, local to SADI-Docker-Galaxy (http://github.com/mikel-egana-aranguren/SADI-Docker-Galaxy). + +**What it does** + +Sample Input:: + + name age superviser + Micheal 42 John + Anne 30 Micheal + +Sample Parameters:: + + Namespace - 'http://localhost/' + Triple 1 - c1 'age' c2(literal) + Triple 2 - c3 'supervises' c1(URI) + +Sample Output:: + + <http://localhost/Michael> <http://localhost/age> "42" + <http://localhost/Anne> <http://localhost/age> "30" + <http://localhost/John> <http://localhost/supervises> <http://localhost/Micheal> + <http://localhost/Micheal> <http://localhost/supervises> <http://localhost/Anne> + +**Output Format** + +Output RDF format is N-Triples by default. + + </help> +</tool>