view extract-partitions.xml @ 48:bcd19db01a6b

fix filter-abund file name

<tool	id="gedlab-khmer-extract-partitions"
	name="Extract partitions"
	version="1.1-1"
	force_history_refresh="true">
	
	<description>
		Separate sequences that are annotated with partitions into grouped files.
	</description>
        <macros>
                <token name="@BINARY@">extract-partitions.py</token>
                <import>macros.xml</import>
        </macros>
        <expand macro="requirements" />
	<command>
mkdir -p output ;
cd output ;
@BINARY@
--max-size $max_size
--min-partition-size $min_partition_size
$output_unasssigned
output
#for input in $inputs
$input
#end for ;
mv output.dist $distribution
	</command>

	<inputs>
		<expand macro="input_sequences_filenames" />
		<param	name="max_size"
			type="integer"
			label="Max group size"
			help="No more than this many number of sequences will be stored in each output"
			value="1000000" />
		<param	name="min_partition_size"
			type="integer"
			label="Min partition size"
			help="The minimum partition size worth keeping"
			value="5" />
		<param	name="output_unassigned"
			type="boolean"
			checked="false"
			truevalue="--output-unassigned"
			falsevalue=""
			label="Output unassigned sequences" />
	</inputs>
	<outputs>
		<data	name="distribution"
			format="text"
			label="Partition size distribution from ${tool.name}" />
		<expand macro="output_sequences" />
	</outputs>
 	<stdio>
        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
		<exit_code	range="1:"
				level="fatal" />
	</stdio>
	
	<tests>
		<test interactor="api">
			<param name="inputs" value="random-20-a.fa.part"/>
			<output name="distribution">
				<assert_contents>
					<has_line_matching expression="'99 1 1 99" />
				</assert_contents>
			</output>
		</test>

	</tests>
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <!--
	<help>
	</help>
    -->    
</tool>