view abundance-dist-single.xml @ 58:be2f355d6841

More citations tweaks

<tool	id="gedlab-khmer-abudance-dist-single"
	name="Abundance Distribution (all-in-one)"
	version="1.1-1"
	force_history_refresh="true">
	
	<description>
		Calculate abundance distribution of the k-mers in a given sequence 
		file.
	</description>
	<macros>
		<token name="@BINARY@">abundance-dist-single.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@
@TABLEPARAMS@
$zero
$bigcount
#if $save_countingtable
--savetable=$optional_output_countingtable
#end if
--report-total-kmers
--squash
@THREADS@
$input_sequence_filename
$output_histogram_filename	
	</command>

	<inputs>
		<expand macro="input_sequence_filename" />
		<param	name="save_countingtable"
			type="boolean"
			label="Save the k-mer counting table(s) in a file"
			help="" />
		<expand macro="input_zero" />
		<param	name="bigcount"
			type="boolean"
			truevalue=""
			falsevalue="--no-bigcount"
			checked="true"
			help="Count k-mers past 255" />
		<expand macro="tableinputs" />
	</inputs>
	<outputs>
		<data	name="optional_output_countingtable"
			format="ct"
			label="${tool.name} k-mer counting table">
			<filter>save_countingtable == True</filter>
		</data>
		<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="type" value="specific" />
		    <param name="tablesize_specific" value="1e7" />
		    <param name="n_tables" value="2" />
		    <param name="ksize" value="17" />
		    <param name="no_zero" value="false" />
		    <output name="output_histogram_filename">
			    <assert_contents>
				    <has_text text="1 96 96 0.98" />
				    <has_text text="1001 2 98 1.0" />
			    </assert_contents>
		    </output>
	    </test>
	    <test>
		    <param name="input_sequence_filename" value="test-abund-read-2.fa" />
		    <param name="type" value="specific" />
		    <param name="tablesize_specific" value="1e7" />
		    <param name="n_tables" value="2" />
		    <param name="ksize" value="17" />
		    <param name="no_zero" value="false" />
		    <param name="bigcount" value="false" />
		    <output name="output_histogram_filename">
			    <assert_contents>
				    <has_text text="1 96 96 0.98" />
				    <has_text text="255 2 98 1.0" />
			    </assert_contents>
		    </output>
	    </test>

    </tests>
    <citations>
	<expand macro="software-citation" />
	<expand macro="counting-citation" />
    </citations>
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <!--
	<help>
	</help>
    -->    
</tool>