comparison featurecounts.xml @ 13:89d097ed772c draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty

12:b2c1799ed8d1

						*#
						"${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'gene_sets' ].get_fields() )[0][2] }"
					#end if
					
					-o "$output"
					-T $threads
					
					#if $extended_parameters.parameters == "extended"
						-t $extended_parameters.gff_feature_type
						-g $extended_parameters.gff_feature_attribute
						$extended_parameters.summarization_level

			<option value="tabdel_default" selected="true">Gene-name "\t" gene-count "\t" gene-length (tab-delimited)</option>
			<option value="tabdel_short">Gene-name "\t" gene-count (tab-delimited)</option>
			<option value="bed">BED format (line per exon): chr "\t" start "\t" stop "\t" description "\t" readcount (tab-delimited)</option>
		</param>
		
		<param name="threads" type="integer" value="2" min="1" label="Number of the CPU threads. Higher numbers only make sense with a higher number of samples." />
		
		<conditional name="extended_parameters">
			<param name="parameters" type="select" label="featureCounts parameters" help="For more advanced featureCounts settings.">
				<option value="default">Default settings</option>
				<option value="extended">Extended settings</option>
			</param>

13:89d097ed772c

						*#
						"${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'gene_sets' ].get_fields() )[0][2] }"
					#end if
					
					-o "$output"
					-T \${GALAXY_SLOTS:-2}
					
					#if $extended_parameters.parameters == "extended"
						-t $extended_parameters.gff_feature_type
						-g $extended_parameters.gff_feature_attribute
						$extended_parameters.summarization_level

			<option value="tabdel_default" selected="true">Gene-name "\t" gene-count "\t" gene-length (tab-delimited)</option>
			<option value="tabdel_short">Gene-name "\t" gene-count (tab-delimited)</option>
			<option value="bed">BED format (line per exon): chr "\t" start "\t" stop "\t" description "\t" readcount (tab-delimited)</option>
		</param>
		
		<conditional name="extended_parameters">
			<param name="parameters" type="select" label="featureCounts parameters" help="For more advanced featureCounts settings.">
				<option value="default">Default settings</option>
				<option value="extended">Extended settings</option>
			</param>