<?xml version="1.0"?>
<tool id="insilico_read_nomalization" name="Insilico Read Normalization" version="r20140717">

<!-- Written by Anmol J. Hemrom -->
<description>Read Normalization</description>
  
    <requirements>
        <requirement type="package" version="r20140717">trinityrnaseq</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>