view abundance-dist.xml @ 34:7611b274ed67

Specify filetypes

<tool	id="gedlab-khmer-abundance-dist"
	name="Abundance Distribution"
	version="1.1-1"
	force_history_refresh="true">
	
	<description>
		Calculate abundance distribution of the k-mers in a given sequence
		file using a pre-made k-mer counting table.
	</description>
        <macros>
		<token name="@BINARY@">abundance-dist.py</token>
		<import>macros.xml</import>
        </macros>
        <expand macro="requirements" />
	<command>
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
mkdir output; cd output;
@BINARY@
--squash
$input_counting_table_filename
$input_sequence_filename
$output_histogram_filename	
	</command>

	<inputs>
		<expand macro="input_sequence_filename" />
		<expand macro="input_counting_table_filename" />
		<expand macro="input_zero" />
	</inputs>
	<outputs>
		<expand macro="abundance-histogram-output" />
	</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>
                    	<param name="input_sequence_filename" value="test-abund-read-2.fa" />
			<param name="input_counting_table_filename" value="test-abund-read-2.ct" ftype="ct" />
			<param name="no_zero" value="false" />
                    	<output name="output_histogram_filename">
				<assert_contents>
					<has_line_matching expression="1 96 96 0.98" />
					<has_line_matching expression="1001 2 98 1.0" />
				</assert_contents>
			</output>
		</test>
		<test>
                    	<param name="input_sequence_filename" value="test-abund-read-2.fa" />
 			<param name="input_counting_table_filename" value="test-abund-read-2.nobigcount.ct" ftype="ct" />
 	                <param name="no_zero" value="false" />
                    	<output name="output_histogram_filename">
                            	<assert_contents>
                                    	<has_line_matching="1 96 96 0.98" />
                                    	<has_line_matching="255 2 98 1.0" />
                            	</assert_contents>
                    	</output>
            	</test>
    	</tests>
    
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <!--
	<help>
	</help>
    -->    
</tool>