comparison genMutModel.xml @ 8:dc383ecbf839 draft

planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty

7:fc1c7b6fb7b6

	## 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 -s ${in_type.reference.fields.path} reference.fa
	#else:
	&& ln ${in_type.reference} reference.fa
	#end if
    && python2 $__tool_directory__/utilities/genMutModel.py
		-r reference.fa
		-m mutation_file.vcf
		-o $genMutModel_modelfile

	</section>
  </inputs>
  <outputs>
	<data format="txt"
		  name="genMutModel_modelfile"
		  label="${os.path.splitext($mutation_file.name)}_genMutModel.p"
		  metadata_source="in_type.reference">
	</data>
	
	<data format="simple"
	      name="trinuc_file"
		  from_work_dir="reference.fa.trinucCounts"
	      label="${os.path.splitext($mutation_file.name)}_trinucCounts.tsv"
	      metadata_source="in_type.reference">
		  <filter>misc['save_trinuc']</filter>
	</data>

  </outputs>

8:dc383ecbf839

	## 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 -s ${in_type.reference.fields.path} reference.fa
	#else:
	&& ln -s ${in_type.reference} reference.fa
	#end if
    && python2 $__tool_directory__/utilities/genMutModel.py
		-r reference.fa
		-m mutation_file.vcf
		-o $genMutModel_modelfile

	</section>
  </inputs>
  <outputs>
	<data format="txt"
		  name="genMutModel_modelfile"
		  label="${os.path.splitext(str($mutation_file.name))[0]}_genMutModel.p"
		  metadata_source="in_type.reference">
	</data>
	
	<data format="simple"
	      name="trinuc_file"
		  from_work_dir="reference.fa.trinucCounts"
	      label="${os.path.splitext(str($mutation_file.name))[0]}_trinucCounts.tsv"
	      metadata_source="in_type.reference">
		  <filter>misc['save_trinuc']</filter>
	</data>

  </outputs>