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comparison genMutModel.xml @ 1:362e0b0f7024 draft

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planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
author thondeboer
date Tue, 15 May 2018 15:32:13 -0400
parents 6e75a84e9338
children 8a739c944dbf
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0:6e75a84e9338 1:362e0b0f7024
4 profile="16.04"> 4 profile="16.04">
5 <description>generates a mutation model based on provided mutations. Creates model file for use in NEAT-genReads</description> 5 <description>generates a mutation model based on provided mutations. Creates model file for use in NEAT-genReads</description>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.9.1">numpy</requirement> 7 <requirement type="package" version="1.9.1">numpy</requirement>
8 <requirement type="package">matplotlib</requirement> 8 <requirement type="package">matplotlib</requirement>
9 <requirement type="package">libgfortran</requirement>
9 </requirements> 10 </requirements>
10 <command detect_errors="exit_code"> 11 <command detect_errors="exit_code">
11 <![CDATA[ 12 <![CDATA[
12 ## Filenames and extensions are important, so make some links to make life easier downstream 13 ## Filenames and extensions are important, so make some links to make life easier downstream
13 ln -s $mutation_file mutation_file.vcf 14 ln -s $mutation_file mutation_file.vcf
14 #if $in_type.input_type == "built-in": 15 #if $in_type.input_type == "built-in":
15 && ln ${in_type.reference.path} reference.fa 16 && ln ${in_type.reference.fields.path} reference.fa
16 #else: 17 #else:
17 && ln ${in_type.reference} reference.fa 18 && ln ${in_type.reference} reference.fa
18 #end if 19 #end if
19 && python2 $__tool_directory__/utilities/genMutModel.py 20 && python2 $__tool_directory__/utilities/genMutModel.py
20 -r reference.fa 21 -r reference.fa