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<tool id="sickle" name="Sickle">
<description>Window Adaptive Trimming of FastQ data</description>
<command>
sickle $readtype.single_or_paired --quiet
#if str($readtype.single_or_paired) == "se":
-f $input_single -t $qual_type -o $output_single
#end if
#if str($readtype.single_or_paired) == "pe":
-f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type
#end if
#if str($qual_threshold) != "":
-q $qual_threshold
#end if
#if str($length_threshold) != "":
-l $length_threshold
#end if
#if str($disable_five_prime) == 'disable_five_prime_true':
-x
#end if
#if str($discard_n) == 'discard_n_true':
-n
#end if
2> /dev/null
</command>
<inputs>
<conditional name="readtype">
<param name="single_or_paired" type="select" optional="false" label="Single-End or Paired-End reads?">
<option value="se" selected="true">Single-End</option>
<option value="pe">Paired-End</option>
</param>
<when value="se">
<param format="fastq, fastqsanger" name="input_single" type="data" optional="false" label="Single-End FastQ Reads"/>
</when>
<when value="pe">
<param format="fastq, fastqsanger" name="input_paired1" type="data" optional="false" label="Paired-End Forward Strand FastQ Reads"/>
<param format="fastq, fastqsanger" name="input_paired2" type="data" optional="false" label="Paired-End Reverse Strand FastQ Reads"/>
</when>
</conditional>
<param name="qual_type" type="select" optional="false" label="Quality type">
<option value="illumina" selected="true">Illumina</option>
<option value="phred">Phred</option>
<option value="sanger">Sanger</option>
</param>
<param name="qual_threshold" value="20" type="integer" optional="true" label="Quality Threshold">
<validator type="in_range" min="0" message="Minimum value is 0"/>
</param>
<param name="length_threshold" value="20" type="integer" optional="true" label="Length Threshold">
<validator type="in_range" min="0" message="Minimum value is 0"/>
</param>
<param name="disable_five_prime" type="boolean" truevalue="disable_five_prime_true" falsevalue="disable_five_prime_false" checked="false" label="Disable 5'-end trimming"/>
<param name="discard_n" type="boolean" truevalue="discard_n_true" falsevalue="discard_n_false" checked="false" label="Discard any sequence with any number of Ns"/>
</inputs>
<outputs>
<data format="fastq" name="output_single" label="Single-End output of ${tool.name} on ${on_string}">
<filter>(readtype['single_or_paired'] == 'se')</filter>
</data>
<data format="fastq" name="output_paired1" label="Paired-End forward strand output of ${tool.name} on ${on_string}">
<filter>(readtype['single_or_paired'] == 'pe')</filter>
</data>
<data format="fastq" name="output_paired2" label="Paired-End reverse strand output of ${tool.name} on ${on_string}">
<filter>(readtype['single_or_paired'] == 'pe')</filter>
</data>
<data format="fastq" name="output_paired_single" label="Singletons from Paired-End output of ${tool.name} on ${on_string}">
<filter>(readtype['single_or_paired'] == 'pe')</filter>
</data>
</outputs>
<help>
</help>
</tool>
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