view SMART/galaxy/WrappGetLetterDistribution.xml @ 31:0ab839023fe4

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<tool id="getLetterDistribution1" name="Get Letter Distribution">
    <description>Calculate distribution for each nucleotide per position for all short reads (S-MART)</description>
    <command interpreter="python">
	    WrappGetLetterDistribution.py -i $inputFileName
	#if $formatType.FormatInputFileName == 'fasta':
		-f fasta
	#else :
		-f fastq
	#end if
	-c $ouputFileNameCSV -a $ouputFileNamePNG1 -b $ouputFileNamePNG2
    </command>
    <inputs>
             <conditional name="formatType">
      			<param name="FormatInputFileName" type="select" label="Input File Format">
	        		<option value="fasta">fasta</option>
       				<option value="fastq" selected="true">fastq</option>
      			</param>
      			<when value="fasta">
             			<param name="inputFileName" format="fasta" type="data" label="Fasta Input File"/>
      			</when>
      			<when value="fastq">
             			<param name="inputFileName" format="fastq" type="data" label="Fastq Input File"/>
      			</when>
             </conditional>
    </inputs>
        
    <outputs>
               	<data name="ouputFileNameCSV" format="tabular" label="[getLetterDistribution] CSV File"/>
               	<data name="ouputFileNamePNG1" format="png" label="[getLetterDistribution] PNG File 1"/>
               	<data name="ouputFileNamePNG2" format="png" label="[getLetterDistribution] PNG File 2"/>
    </outputs>
    <tests>
    	<test>
            <param name="FormatInputFileName" value="fastq" />
            <param name="inputFileName" value="short_fastq.fastq" />
            <output name="outputFileNameCSV" file="exp_getletterdistribution_short_fastq.csv" />     
        </test>
    </tests>
</tool>