Mercurial > repos > jjkoehorst > sapp

annotate conversion/gbk2rdf/gbktordf.xml @ 24:9610ddbca991

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author jjkoehorst <jasperkoehorst@gmail.com>
date Sat, 21 Feb 2015 19:25:28 +0100
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1 <tool id="SAPP_genbank_to_ttl" name="EMBL/GBK to RDF" version="0.1">
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2 <requirements>
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3 <requirement type='package' version="3.4">python</requirement>
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4 <requirement type='package' version="1.0">rdflib</requirement>
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5 </requirements>
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6 <description>Genbank to RDF conversion</description>
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7 <command interpreter="python3.4">gbktordf.py '-input' '$input' -output '$output' -sourcedb "$format" -format "$format"</command>
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8 <inputs>
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9 <param name="input" type="data" format="gbk,gb,genbank,embl" label="Genbank file"/>
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10 <param name="format" type="select" label="EMBL/GBK">
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11 <option value="genbank" selected="true"> Genbank</option>
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12 <option value="embl"> EMBL </option>
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13 </param>
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14 </inputs>
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16 <outputs>
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17 <data format="rdf" name="output" label="GBKttl: ${input.name}" />
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18 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input" value="test-data/NC_010067.gbk"/>
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23 <output name="$output" file="NC_010067.rdf"/>
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24 <output name="$format" value="genbank"/>
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25 <output name="$sourcedb" value="genbank"/>
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26 </test>
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27 <test>
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28 <param name="input" value="test-data/CP009049.embl"/>
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29 <output name="$output" file="CP009049.rdf"/>
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30 <output name="$format" value="embl"/>
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31 <output name="$sourcedb" value="embl"/>
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32 </test>
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33 </tests>
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35 <help>
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36 Genbank or EMBL to RDF conversion
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37 </help>
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38 </tool>