annotate rapsodyn/PrepareFastqLight.xml~ @ 7:3f7b0788a1c4 draft

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<tool id="PrepareFastqLight" name="PrepareFastqLight" version="1.01">
<description>Fastq preparation</description>
<command interpreter="perl">
    PrepareFastqLight.pl -read1_file $input_read1_file -read2_file $input_read2_file -output1 $output_read1_file -output2 $output_read2_file -log_file $log_file -type $quality_type -min_quality $min_quality -min_length $min_length
</command>
<inputs>
	<param name="input_read1_file"  type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/>
	<param name="input_read2_file"  type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/>
	<param name="quality_type" type="select" label="Select input quality format">
		<option value="sanger">Sanger</option>
		<option value="illumina">Illumina 1.3-1.7</option>
	</param>
	<param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/>
	<param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/>
</inputs>
<outputs>
	<data name="output_read1_file" format="fastqsanger" label="${tool.name} on ${on_string}"/>
	<data name="output_read2_file" format="fastqsanger" label="${tool.name} on ${on_string}"/>
	<data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
</outputs>

<help>



</help>
</tool>