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comparison genMutModel.xml @ 8:dc383ecbf839 draft

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planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
author thondeboer
date Tue, 15 May 2018 23:09:17 -0400
parents fc1c7b6fb7b6
children 441103f02a11
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7:fc1c7b6fb7b6 8:dc383ecbf839
12 ## Filenames and extensions are important, so make some links to make life easier downstream 12 ## Filenames and extensions are important, so make some links to make life easier downstream
13 ln -s $mutation_file mutation_file.vcf 13 ln -s $mutation_file mutation_file.vcf
14 #if $in_type.input_type == "built-in": 14 #if $in_type.input_type == "built-in":
15 && ln -s ${in_type.reference.fields.path} reference.fa 15 && ln -s ${in_type.reference.fields.path} reference.fa
16 #else: 16 #else:
17 && ln ${in_type.reference} reference.fa 17 && ln -s ${in_type.reference} reference.fa
18 #end if 18 #end if
19 && python2 $__tool_directory__/utilities/genMutModel.py 19 && python2 $__tool_directory__/utilities/genMutModel.py
20 -r reference.fa 20 -r reference.fa
21 -m mutation_file.vcf 21 -m mutation_file.vcf
22 -o $genMutModel_modelfile 22 -o $genMutModel_modelfile
113 </section> 113 </section>
114 </inputs> 114 </inputs>
115 <outputs> 115 <outputs>
116 <data format="txt" 116 <data format="txt"
117 name="genMutModel_modelfile" 117 name="genMutModel_modelfile"
118 label="${os.path.splitext($mutation_file.name)}_genMutModel.p" 118 label="${os.path.splitext(str($mutation_file.name))[0]}_genMutModel.p"
119 metadata_source="in_type.reference"> 119 metadata_source="in_type.reference">
120 </data> 120 </data>
121 121
122 <data format="simple" 122 <data format="simple"
123 name="trinuc_file" 123 name="trinuc_file"
124 from_work_dir="reference.fa.trinucCounts" 124 from_work_dir="reference.fa.trinucCounts"
125 label="${os.path.splitext($mutation_file.name)}_trinucCounts.tsv" 125 label="${os.path.splitext(str($mutation_file.name))[0]}_trinucCounts.tsv"
126 metadata_source="in_type.reference"> 126 metadata_source="in_type.reference">
127 <filter>misc['save_trinuc']</filter> 127 <filter>misc['save_trinuc']</filter>
128 </data> 128 </data>
129 129
130 </outputs> 130 </outputs>