# HG changeset patch
# User jjkoehorst
# Date 1467181307 14400
# Node ID f2cbf1230026c5ad62575943d83fb2b0481d11f8
# Parent  174e4bfea91593249852b7db5b7c4bd68fb50690
Uploaded

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
@@ -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>
+