<commit_before><?xml version="1.0" encoding="UTF-8"?>

<iridaWorkflow>
	<id>2b9cf250-926a-41a0-b5ea-f71a3fd206e0</id>
	<name>AssemblyAnnotationCollection</name>
	<version>0.1</version>
	<analysisType>assembly-annotation-collection</analysisType>
	<inputs>
		<sequenceReadsPaired>sequence_reads_paired</sequenceReadsPaired>
	</inputs>
	<parameters>
		<parameter name="read-merge-min-overlap" defaultValue="20">
			<toolParameter
				toolId="irida.corefacility.ca/galaxy-shed/repos/irida/flash/FLASH/1.3.0"
				parameterName="min_overlap" />
		</parameter>
		<parameter name="read-merge-max-overlap" defaultValue="300">
			<toolParameter
				toolId="irida.corefacility.ca/galaxy-shed/repos/irida/flash/FLASH/1.3.0"
				parameterName="max_overlap" />
		</parameter>
		<parameter name="assembly-kmers" defaultValue="21,33,55,77,99,127">
			<toolParameter
				toolId="toolshed.g2.bx.psu.edu/repos/lionelguy/spades/spades/1.0"
				parameterName="kmers" />
		</parameter>
		<parameter name="assembly-contig-min-length" defaultValue="1000">
			<toolParameter
				toolId="irida.corefacility.ca/galaxy-shed/repos/irida/filter_spades_repeats/filter_spades_repeat/1.0.0"
				parameterName="len_cutoff" />
		</parameter>
		<parameter name="assembly-contig-min-coverage-ratio"
			defaultValue="0.33">
			<toolParameter
				toolId="irida.corefacility.ca/galaxy-shed/repos/irida/filter_spades_repeats/filter_spades_repeat/1.0.0"
				parameterName="cov_cutoff" />
		</parameter>
		<parameter name="assembly-contig-min-repeat-coverage-ratio"
			defaultValue="1.75">
			<toolParameter
				toolId="irida.corefacility.ca/galaxy-shed/repos/irida/filter_spades_repeats/filter_spades_repeat/1.0.0"
				parameterName="rep_cutoff" />
		</parameter>
		<parameter name="assembly-contig-min-length-coverage-calculation"
			defaultValue="5000">
			<toolParameter
				toolId="irida.corefacility.ca/galaxy-shed/repos/irida/filter_spades_repeats/filter_spades_repeat/1.0.0"
				parameterName="cov_len_cutoff" />
		</parameter>
		<parameter name="annotation-similarity-e-value-cutoff"
			defaultValue="1e-06">
			<toolParameter
				toolId="toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.4.0"
				parameterName="evalue" />
		</parameter>
	</parameters>
	<outputs>
		<output name="read-merge-log" fileName="flash-combined.log.zip" />
		<output name="assembly-log" fileName="spades-combined.log.zip" />
		<output name="filter-assembly-log" fileName="filter-spades-combined.txt.zip" />
		<output name="contigs-all" fileName="contigs-all-combined.fasta.zip" />
		<output name="contigs-with-repeats" fileName="contigs-with-repeats-combined.fasta.zip" />
		<output name="contigs-without-repeats" fileName="contigs-without-repeats-combined.fasta.zip" />
		<output name="assembly-stats-repeats" fileName="assembly-stats-with-repeats-combined.tsv" />
		<output name="annotations-genbank" fileName="genome.gbk-combined.zip" />
		<output name="annotations-stats" fileName="prokka_stats-combined.txt.zip" />
		<output name="annotations-log" fileName="prokka-combined.log.zip" />
		<output name="annotations-error" fileName="prokka-combined.err.zip" />
	</outputs>
	<toolRepositories>
		<repository>
			<name>flash</name>
			<owner>irida</owner>
			<url>https://irida.corefacility.ca/galaxy-shed</url>
			<revision>4287dd541327</revision>
		</repository>
		<repository>
			<name>filter_spades_repeats</name><commit_msg>Fixed up name for annotations-genbank<commit_after><?xml version="1.0" encoding="UTF-8"?>

<iridaWorkflow>
	<id>2b9cf250-926a-41a0-b5ea-f71a3fd206e0</id>
	<name>AssemblyAnnotationCollection</name>
	<version>0.1</version>
	<analysisType>assembly-annotation-collection</analysisType>
	<inputs>
		<sequenceReadsPaired>sequence_reads_paired</sequenceReadsPaired>
	</inputs>
	<parameters>
		<parameter name="read-merge-min-overlap" defaultValue="20">
			<toolParameter
				toolId="irida.corefacility.ca/galaxy-shed/repos/irida/flash/FLASH/1.3.0"
				parameterName="min_overlap" />
		</parameter>
		<parameter name="read-merge-max-overlap" defaultValue="300">
			<toolParameter
				toolId="irida.corefacility.ca/galaxy-shed/repos/irida/flash/FLASH/1.3.0"
				parameterName="max_overlap" />
		</parameter>
		<parameter name="assembly-kmers" defaultValue="21,33,55,77,99,127">
			<toolParameter
				toolId="toolshed.g2.bx.psu.edu/repos/lionelguy/spades/spades/1.0"
				parameterName="kmers" />
		</parameter>
		<parameter name="assembly-contig-min-length" defaultValue="1000">
			<toolParameter
				toolId="irida.corefacility.ca/galaxy-shed/repos/irida/filter_spades_repeats/filter_spades_repeat/1.0.0"
				parameterName="len_cutoff" />
		</parameter>
		<parameter name="assembly-contig-min-coverage-ratio"
			defaultValue="0.33">
			<toolParameter
				toolId="irida.corefacility.ca/galaxy-shed/repos/irida/filter_spades_repeats/filter_spades_repeat/1.0.0"
				parameterName="cov_cutoff" />
		</parameter>
		<parameter name="assembly-contig-min-repeat-coverage-ratio"
			defaultValue="1.75">
			<toolParameter
				toolId="irida.corefacility.ca/galaxy-shed/repos/irida/filter_spades_repeats/filter_spades_repeat/1.0.0"
				parameterName="rep_cutoff" />
		</parameter>
		<parameter name="assembly-contig-min-length-coverage-calculation"
			defaultValue="5000">
			<toolParameter
				toolId="irida.corefacility.ca/galaxy-shed/repos/irida/filter_spades_repeats/filter_spades_repeat/1.0.0"
				parameterName="cov_len_cutoff" />
		</parameter>
		<parameter name="annotation-similarity-e-value-cutoff"
			defaultValue="1e-06">
			<toolParameter
				toolId="toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.4.0"
				parameterName="evalue" />
		</parameter>
	</parameters>
	<outputs>
		<output name="read-merge-log" fileName="flash-combined.log.zip" />
		<output name="assembly-log" fileName="spades-combined.log.zip" />
		<output name="filter-assembly-log" fileName="filter-spades-combined.txt.zip" />
		<output name="contigs-all" fileName="contigs-all-combined.fasta.zip" />
		<output name="contigs-with-repeats" fileName="contigs-with-repeats-combined.fasta.zip" />
		<output name="contigs-without-repeats" fileName="contigs-without-repeats-combined.fasta.zip" />
		<output name="assembly-stats-repeats" fileName="assembly-stats-with-repeats-combined.tsv" />
		<output name="annotations-genbank" fileName="genome-combined.gbk.zip" />
		<output name="annotations-stats" fileName="prokka_stats-combined.txt.zip" />
		<output name="annotations-log" fileName="prokka-combined.log.zip" />
		<output name="annotations-error" fileName="prokka-combined.err.zip" />
	</outputs>
	<toolRepositories>
		<repository>
			<name>flash</name>
			<owner>irida</owner>
			<url>https://irida.corefacility.ca/galaxy-shed</url>
			<revision>4287dd541327</revision>
		</repository>
		<repository>
			<name>filter_spades_repeats</name>
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