Mercurial > repos > thondeboer > neat_genreads

diff genMutModel.xml @ 10:7d10b55965c9 draft default tip

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planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
author thondeboer
date Wed, 16 May 2018 17:02:51 -0400
parents 441103f02a11
children
line wrap: on
line diff
--- a/genMutModel.xml	Wed May 16 02:05:26 2018 -0400
+++ b/genMutModel.xml	Wed May 16 17:02:51 2018 -0400
@@ -50,7 +50,7 @@
 			   type="select"
 			   label="Select a built-in reference sequence"
 			   help="The reference sequence that will be used as the basis for the simulated reads">
-		  <options from_data_table="all_fasta" />
+		  <options from_data_table="fasta_indexes" />
 		</param>
 	  </when>
 	  <when value="history">
@@ -180,5 +180,16 @@
 			<output name="trinuc_file" value="chrMT.fa.trinucCounts" compare="diff"/>
 		</test>
 
+		<test>
+			<conditional name="in_type">
+				<param name="input_type" value="built-in"/>
+			  <param name="reference" value="hg19chrmt" format="fasta">
+			     <options from_data_table="fasta_indexes" />
+			  </param>
+			</conditional>
+			<param name="mutation_file" value="chrMT-PE-VCF-BAM.vcf"/>
+			<output name="genMutModel_modelfile" value="chrMT-PE-VCF-BAM-genMutModel.p" compare="diff"/>
+		</test>
+		
 	</tests>
 </tool>
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