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<?xml version="1.0"?>
<tool id="insilico_read_nomalization" name="Insilico Read Normalization" version="0.0.1">

<description>Read Normalization</description>
<requirements>
        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
        <requirement type="set_environment">TRINITY_HOME</requirement>

</requirements>
<command interperter="perl"> \$TRINITY_HOME/util/insilico_read_normalization.pl
--JM $JM
--max_cov $maximum_coverage

## Inputs.
#if str($inputs.paired_or_single) == "paired":

	--left $inputs.left_input --right $inputs.right_input

	#if  $inputs.left_input.ext == 'fa':
		--seqType fa
	#else:
		--seqType fq
	#end if

	## Additional parameters.
	#if str($inputs.additional_params.use_additional) == "yes":

		#if str($inputs.additional_params.library_type) != "None":
			--SS_lib_type $inputs.additional_params.library_type
		#end if
		
		$inputs.additional_params.pairs_together
		--CPU $inputs.additional_params.CPU
		$inputs.additional_params.PARALLEL_STATS
		--KMER_SIZE $inputs.additional_params.KMER_SIZE
		--max_pct_stdev $inputs.additional_params.max_pct_stdev

	#end if


#else:

	--single $inputs.input

	#if  str($inputs.input.ext) == 'fa':
		--seqType fa
	#else:
		--seqType fq
	#end if

	## Additional parameters.
	#if str($inputs.additional_params.use_additional) == "yes":

		#if str($inputs.additional_params.library_type) != "None":
			--SS_lib_type $inputs.additional_params.library_type
		#end if
		
		##$inputs.additional_params.pairs_together
		--CPU $inputs.additional_params.CPU
		##$inputs.additional_params.PARALLEL_STATS
		--KMER_SIZE $inputs.additional_params.KMER_SIZE
		--max_pct_stdev $inputs.additional_params.max_pct_stdev

	#end if

#end if



## direct to output
&gt; $insilico_read_normalization_log 2&gt;&amp;1

</command>

<inputs>
	<param name="JM" type="select" label="JM" help="--JM &lt; string &gt; ; Amount of memory to allocate to Jellyfish for Kmer catalog construction">
		<option value="1G">1G</option>
		<option value="10G">10G</option>
		<option value="20G">20G</option>
		<option value="50G">50G</option>
	</param>

	<param name="maximum_coverage" type="integer" value="25" label="Maximum Coverage" help="--max_cov &lt; int &gt; ; targeted maximum coverage for reads"/>

	<conditional name="inputs">
		<param name="paired_or_single" type="select" label="Paired or Single-end data?">
			<option value="paired">Paired</option>
			<option value="single">Single</option>
		</param>

		<when value="paired">
			<param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
			<param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>

			<conditional name="additional_params">
				<param name="use_additional" type="select" label="Use Additional Params?">
					<option value="no">No</option>
					<option value="yes">Yes</option>
				</param>
				<when value="no"/>
				<when value="yes">
					<param name="library_type" type="select" label="Strand-specific Library Type">
						<option value="None">None</option>
						<option value="FR">FR</option>
						<option value="RF">RF</option>
					</param>
					<param name="pairs_together" type="boolean" label="--pairs_together" help="process paired reads by averaging stats between pairs and retaining linking info" truevalue="--pairs_together" falsevalue="" checked="true" />
					<param name="CPU" type="integer" value="2" min="1" max="30" label="CPU" help="--CPU &lt; int &gt; ; Number of CPUs to use (Maximum limit is 30 core)" />
					<param name="PARALLEL_STATS" type="boolean" label="--PARALLEL_STATS"  help="Generate read stats in parallel for paired reads" truevalue="--PARALLEL_STATS" falsevalue="" checked="true" />
					<param name="KMER_SIZE" type="integer"  value="25" label="--KMER SIZE" help="Default is 25" />
					<param name="max_pct_stdev" type="integer"  value="200" label="--max_pct_stdev" help="maximum pct of mean for stdev of kmer coverage across read"/>
				</when>
			</conditional>
		</when>

		<when value="single">
			<param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>

			<conditional name="additional_params">
				<param name="use_additional" type="select" label="Use Additional Params?">
					<option value="no">No</option>
					<option value="yes">Yes</option>
				</param>
				<when value="no"/>
				<when value="yes">
					<param name="library_type" type="select" label="Strand-specific Library Type">
						<option value="None">None</option>
						<option value="F">F</option>
						<option value="R">R</option>
					</param>
					<param name="CPU" type="integer" value="2" min="1" max="30" label="CPU" help="--CPU &lt; int &gt; ; Number of CPUs to use (Maximum limit is 30 core)" />
					<param name="KMER_SIZE" type="integer"  value="25" label="--KMER SIZE" help="Default is 25" />
					<param name="max_pct_stdev" type="integer"  value="200" label="--max_pct_stdev" help="maximum pct of mean for stdev of kmer coverage across read"/>
				</when>
			</conditional>
		</when>
	</conditional>


</inputs>

<outputs>
<data format="txt" name="insilico_read_normalization_log" label="${tool.name} on ${on_string}: log" />
<data format="fastq"  name="left_normalized_read"  label="${tool.name} on ${on_string}: Left  Read" from_work_dir="left.norm.fq"/>
<data format="fastq"  name="right_normalized_read" label="${tool.name} on ${on_string}: Right Read" from_work_dir="right.norm.fq"/>
</outputs>


<tests/>
<help>Insilico Read Normalization</help>

</tool>