| Previous changeset 33:174e4bfea915 (2016-06-29) Next changeset 35:fa736576c7ed (2016-07-04) |
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added:
fasta2rdf.xml |
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| diff -r 174e4bfea915 -r f2cbf1230026 fasta2rdf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta2rdf.xml Wed Jun 29 02:21:47 2016 -0400 |
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| @@ -0,0 +1,82 @@ +<tool id="DFASTA2RDF" name="FASTA to RDF" version="0.1"> + <description>SAPP - FASTA 2 RDF conversion</description> + <requirements> + <container type="docker">jjkoehorst/sappdocker:FASTA2RDF</container> + </requirements> + + <command>java -jar /fasta2rdf/target/FASTA2RDF-0.1-jar-with-dependencies.jar + '--type' '$source.fastaType' '--ignorestop' '$IgnoreStopCodon' + '--input' '$input' '--output' '$output' '-organism' '$organism' + '--ncbi_taxid' '$ncbi_taxid' + #if len(str($identification_tag))==0 + '--idtag' ${input.name} + #else + '--idtag' '$identification_tag' + #end if + --source SAPP + + #for $index, $id in enumerate( $ids ) + '--id_alternative' '$id.id_tag' + #end for + '--id_alternative' '$input.name' + '--codon' '$table' + </command> + <inputs> + <param size="60" name="input" type="data" format="fasta" label="Fasta file for conversion" /> + + <conditional name="source"> + <param name="fastaType" type="select" + label="Select if it is a Genome/Gene/Protein or program wont start!"> + <option value="">To be chosen</option> + <option value="genome"> Genome </option> + <option value="gene"> Gene</option> + <option value="protein"> Protein </option> + <validator type="empty_field" message="Please select if it is a Genome, Gene or Protein" /> + </param> + </conditional> + + <param name="table" type="select" label="Codon table"> + <option value="1"> 1 - UNIVERSAL </option> + <option value="2"> 2 - VERTEBRATE_MITOCHONDRIAL </option> + <option value="3"> 3 - YEAST_MITOCHONDRIAL </option> + <option value="4"> 4 - MOLD_MITOCHONDRIAL </option> + <option value="5"> 5 - INVERTEBRATE_MITOCHONDRIAL </option> + <option value="6"> 6 - CILIATE_NUCLEAR </option> + <option value="9"> 9 - ECHINODERM_MITOCHONDRIAL </option> + <option value="10"> 10 - EUPLOTID_NUCLEAR </option> + <option value="11" selected="true"> 11 - BACTERIAL </option> + <option value="12"> 12 - ALTERNATIVE_YEAST_NUCLEAR </option> + <option value="13"> 13 - ASCIDIAN_MITOCHONDRIAL </option> + <option value="14"> 14 - FLATWORM_MITOCHONDRIAL </option> + <option value="15"> 15 - BLEPHARISMA_MACRONUCLEAR </option> + <option value="16"> 16 - 2CHLOROPHYCEAN_MITOCHONDRIAL </option> + <option value="21"> 21 - TREMATODE_MITOCHONDRIAL </option> + <option value="23"> 23 - SCENEDESMUS_MITOCHONDRIAL </option> + </param> + <param size="60" name="organism" type="text" format="text" + label="organism name" /> + <param name='IgnoreStopCodon' type='boolean' + label='Ignore if stop codon within protein sequence' truevalue='true' + falsevalue='false' checked="false" help='' /> + + <param size="60" name="ncbi_taxid" type="integer" value="0" + label="NCBI taxonomy ID" optional="False"> + <validator type="in_range" min="1" + message="Minimum taxonomy value is 1" /> + </param> + <param size="60" name="identification_tag" type="text" format="text" + label="An identification tag used for RDF storage !Needs to be very unique!" + optional="True" /> + <repeat name="ids" title="Identification tags"> + <param size="60" name="id_tag" type="text" format="text" + label="An identification tag used by other consortiums" /> + </repeat> + </inputs> + <outputs> + <data format="ttl" name="output" label="FASTA2RDF: ${input.name}" /> + </outputs> + <help> + RDF creation from a multi (gene/protein/genome) fasta file + </help> +</tool> + |