Mercurial > repos > mikel-egana-aranguren > sadi_docker
diff tools/SADI-Docker/SADI-Docker-tab2rdf.xml @ 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 |
line wrap: on
line diff
--- /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 EgaƱa 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>