# HG changeset patch
# User thondeboer
# Date 1526412733 14400
# Node ID 362e0b0f7024c7f8a8c212b48f9925d9842fc703
# Parent  6e75a84e9338c1f7c0d56f32bada6056365596a6
planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty

diff -r 6e75a84e9338 -r 362e0b0f7024 computeFraglen.xml
--- a/computeFraglen.xml	Tue May 15 02:39:53 2018 -0400
+++ b/computeFraglen.xml	Tue May 15 15:32:13 2018 -0400
@@ -6,6 +6,7 @@
   <requirements>
     <requirement type="package" version="0.1.19">samtools</requirement>
     <requirement type="package" version="1.9.1">numpy</requirement>
+	<requirement type="package">libgfortran</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
diff -r 6e75a84e9338 -r 362e0b0f7024 computeGC.xml
--- a/computeGC.xml	Tue May 15 02:39:53 2018 -0400
+++ b/computeGC.xml	Tue May 15 15:32:13 2018 -0400
@@ -6,12 +6,13 @@
   <requirements>
     <requirement type="package" version="2.25.0">bedtools</requirement>
     <requirement type="package" version="1.9.1">numpy</requirement>
+	<requirement type="package">libgfortran</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
     bedtools genomecov -d -ibam $bam_file
 		#if $in_type.input_type == "built-in":
-		  -g ${in_type.reference.path}
+		  -g ${in_type.reference.fields.path}
 		#else:
 		  -g ${in_type.reference}
 		#end if
diff -r 6e75a84e9338 -r 362e0b0f7024 genMutModel.xml
--- a/genMutModel.xml	Tue May 15 02:39:53 2018 -0400
+++ b/genMutModel.xml	Tue May 15 15:32:13 2018 -0400
@@ -6,13 +6,14 @@
   <requirements>
     <requirement type="package" version="1.9.1">numpy</requirement>
     <requirement type="package">matplotlib</requirement>
+	<requirement type="package">libgfortran</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
 	## Filenames and extensions are important, so make some links to make life easier downstream
 	ln -s $mutation_file mutation_file.vcf
 	#if $in_type.input_type == "built-in":
-	&& ln ${in_type.reference.path} reference.fa
+	&& ln ${in_type.reference.fields.path} reference.fa
 	#else:
 	&& ln ${in_type.reference} reference.fa
 	#end if
diff -r 6e75a84e9338 -r 362e0b0f7024 genSeqErrorModel.xml
--- a/genSeqErrorModel.xml	Tue May 15 02:39:53 2018 -0400
+++ b/genSeqErrorModel.xml	Tue May 15 15:32:13 2018 -0400
@@ -6,6 +6,7 @@
   <requirements>
     <requirement type="package" version="1.9.1">numpy</requirement>
     <requirement type="package">matplotlib</requirement>
+	<requirement type="package">libgfortran</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
diff -r 6e75a84e9338 -r 362e0b0f7024 neat_genreads.xml
--- a/neat_genreads.xml	Tue May 15 02:39:53 2018 -0400
+++ b/neat_genreads.xml	Tue May 15 15:32:13 2018 -0400
@@ -5,12 +5,13 @@
   <description>is a fine-grained read simulator</description>
   <requirements>
     <requirement type="package" version="1.9.1">numpy</requirement>
+	<requirement type="package">libgfortran</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
     python2 $__tool_directory__/genReads.py
 		#if $in_type.input_type == "built-in":
-		  -r ${in_type.reference.path}
+		  -r ${in_type.reference.fields.path}
 		#else:
 		  -r ${in_type.reference}
 		#end if