view filter-below-abund.xml @ 58:be2f355d6841

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<tool	id="gedlab-khmer-filter-below-abund"
	name="Filter below abundance cutoff of 50"
	version="1.1-1"
	force_history_refresh="true">
	
	<description>
		Trims fastq/fasta sequences at k-mers with abundance below 50
		based on a provided k-mer counting table.
	</description>
	<macros>
		<token name="@BINARY@">filter-below-abund.py</token>
		<import>macros.xml</import>
	</macros>
	<expand macro="requirements" />
	<command>
mkdir output; cd output;
@BINARY@
$input_counting_table_filename
#for input in $inputs
 $input
#end for
	</command>

	<inputs>
		<expand macro="input_sequences_filenames" />
		<expand macro="input_counting_table_filename" />	
	</inputs>
	<outputs>
		<!-- <expand macro="output_sequences" /> -->
		<expand macro="output_sequences_single" />
	</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="test-abund-read-2.fa" />
                        <param name="input_counting_table_filename" value="test-abund-read-2.ct" ftype="ct" />
                        <output name="output">
				<discover_dataset name="test-abund-read-2.fa.abundfilt">
				</discover_dataset>
                        </output>
                </test>
                <test interactor="api">
                        <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="cutoff" value="1" />
                        <output name="output">
				<discover_dataset name="test-abund-read-2.fa.abundfilt">
                                	<assert_contents>
                                        	<has_text text="GGTTGACGGGGCTCAGGG" />
                                	</assert_contents>
				</discover_dataset>
                        </output>
                </test>
	</tests> -->
	<citations>
		<expand macro="software-citation" />
		<expand macro="counting-citation" />
	</citations>
	<!-- [OPTIONAL] ReST Help displayed in Galaxy -->
    <!--
	<help>
	</help>
    -->    
</tool>