# HG changeset patch
# User cpt
# Date 1653004944 0
# Node ID dca61f5e2d43d102e399590a9ab88fcb900c83dd
# Parent  45a5cf6b0ff4fadb775fe0f1a9ef1841f6e6dbd9
Uploaded

diff -r 45a5cf6b0ff4 -r dca61f5e2d43 cpt_req_phage_start/macros.xml
--- a/cpt_req_phage_start/macros.xml	Fri May 13 05:31:56 2022 +0000
+++ b/cpt_req_phage_start/macros.xml	Fri May 20 00:02:24 2022 +0000
@@ -28,20 +28,7 @@
 	<param label="Genome Annotations" name="gff3" type="data" format="gff3" />
 	</xml>
 	<xml name="genome_selector">
-		<conditional name="reference_genome">
-			<param name="reference_genome_source" type="select" label="Reference Genome">
-				<option value="history" selected="True">From History</option>
-				<option value="cached">Locally Cached</option>
-			</param>
-			<when value="cached">
-				<param name="fasta_indexes" type="select" label="Source FASTA Sequence">
-					<options from_data_table="all_fasta"/>
-				</param>
-			</when>
-			<when value="history">
-				<param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
-			</when>
-		</conditional>
+	    <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
 	</xml>
 	<xml name="gff3_input">
 		<param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
@@ -54,23 +41,13 @@
 	"$gff3_data"
 	</token>
 	<token name="@INPUT_FASTA@">
-#if str($reference_genome.reference_genome_source) == 'cached':
-		"${reference_genome.fasta_indexes.fields.path}"
-#else if str($reference_genome.reference_genome_source) == 'history':
 		genomeref.fa
-#end if
 	</token>
 	<token name="@GENOME_SELECTOR_PRE@">
-#if $reference_genome.reference_genome_source == 'history':
-		ln -s $reference_genome.genome_fasta genomeref.fa;
-#end if
+		ln -s $genome_fasta genomeref.fa;
 	</token>
 	<token name="@GENOME_SELECTOR@">
-#if str($reference_genome.reference_genome_source) == 'cached':
-		"${reference_genome.fasta_indexes.fields.path}"
-#else if str($reference_genome.reference_genome_source) == 'history':
 		genomeref.fa
-#end if
 	</token>
         <xml name="input/fasta">
 		<param label="Fasta file" name="sequences" type="data" format="fasta"/>