view count-median.xml @ 57:61e12ac81cd9

Add citation for count-median; change diginorm to @unpublished

<tool	id="gedlab-khmer-count-median"
	name="Count Median"
	version="1.1-1"
	force_history_refresh="true">
	
	<description>
		Count the median/avg k-mer abundance for each sequence in the input file,
		based on the k-mer counts in the given k-mer counting table. Can be used to
		estimate expression levels (mRNAseq) or coverage (genomic/metagenomic).
	</description>
        <macros>
		<token name="@BINARY@">count-median.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@
		$input_counting_table_filename
		$input_sequence_filename
		$output_summary_filename	
	</command>

	<inputs>
		<expand macro="input_sequence_filename" />
		<expand macro="input_counting_table_filename" />
	</inputs>
	<outputs>
		<data name="output_summary_filename" format="text" label="${input_sequence_filename} sequence id, median, average, stddev, and seq length" />
	</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="input_sequence_filename" value="test-abund-read-2.fa" />
                        <param name="input_counting_table_filename" value="test-abund-read-2.ct" ftype="ct" />
                        <output name="output_summary_filename">
                                <assert_contents>
                                        <has_line_matching expression="seq 1001 1001.0 0.0 18" />
                                        <has_line_matching expression="895:1:37:17593:9954/1 1 103.803741455 303.702941895 114" />
                                </assert_contents>
                        </output>
		</test>
	</tests>
	<citations>
		<expand macro="software-citation" />
		<expand macro="diginorm-citation" />
	</citations>
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <!--
	<help>
	</help>
    -->    
</tool>