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<tool id='id_transDecoder' name='transDecoder' version='1.0'>
<description> coding region </description>
<!--requirement></requirement-->
<requirements>
        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
        <requirement type="set_environment">TRINITY_HOME</requirement>

</requirements>
<command>perl \$TRINITY_HOME/trinity-plugins/transdecoder/TransDecoder
	
	-t $transcript
	
	#if str($optional.parameters) == 'yes':
		#if ($train):
			--train $train
		#end if

		#if ($min_protein_length):
			-m $min_protein_length
		#end if

		#if ($genetic_code):
			-G $genetic_code
		#end if

		#if ($strand-specific):
			$strand-specific	
		#end if

		#if ($lottmn):
			-T $lottmm	
		#end if

		#if ($retain_long_orfs):
			--retain_long_orfs $retain_long_orfs
		#end if
	#end if

	#if str($pfam.options) == 'yes':
		#if ($pfam_db):
			--search_pfam $pfam_db
		#end if

		#if ($CPU):
			--CPU $CPU
		#end if
	#end if	
	
	##log file
	&gt; $transdecoder_log 2&gt;&amp;1;


	## output renaming

	cp -s dataset_*.dat.transdecoder.pep transcript.transdecoder.pep;
	cp -s dataset_*.dat.transdecoder.cds transcript.transdecoder.cds;
	cp -s dataset_*.dat.transdecoder.bed transcript.transdecoder.bed;
	cp -s dataset_*.dat.transdecoder.gff3 transcript.transdecoder.gff3;
	cp -s dataset_*.dat.transdecoder.mRNA transcript.transdecoder.mRNA;
</command>

<inputs>
 <!-- Required -->

  <param name='transcript' type='data' label='Transcripts [ in fasta format ]' help=' -t &lt; string &gt; ; Assembled reads in fasta file format'/>

 <!-- Optional -->

 <conditional name='optional'>
 	<param name='parameters' type='select' label='Use Optional Parameters'>
 		<option value='no'>NO</option>
 		<option value='yes'>YES</option>
 	</param>
 	<when value='no'/>
	<when value='yes'>
  		<param name='train' type='data' optional='true' label='FASTA file with ORFs to train Markov Mod for protein identification' help='--train &lt; string &gt; ; FASTA file with ORFs to train Markov Mod for protein identification; otherwise longest non-redundant ORFs used' />
		<param name='min_protein_length' type='integer' optional='true' value='100' label='Minimum Protein Length' help='-m &lt; int &gt; ;minimum protein length (default: 100)'/>
		<param name='genetic_code' type='select' optional='true' label='Select Genetic Code' help=' -G &lt; string &gt; ; genetic code (default is "universal")'>
			<option value='universal' selected='true'>Universal</option>
			<option value='Euplotes'>Euplotes</option>
			<option value='Tetrahymena'>Tetrahymena</option>
			<option value='Candida'>Candida</option>
			<option value='Acetabularia'>Acetabularia</option>
  		</param>
  		<param name='strand-specific' type='boolean' truevalue='-S' falsevalue='' optional='true' label='Strand-Specific [ -S ]' help='strand-specific (only analyzes top strand)'/> 
  		<param name='lottmm' type='integer' optional='true' value='500' label=' -T ; Needs a label ??? ' help='-T &lt; int &gt; ; If no --train, top longest ORFs to train Markov Model (hexamer stats) (default: 500)'/>	
  		<param name='retain_long_orfs' type="integer" optional='true' value="900" label=' --retain_long_orfs ; Needs a label ??? ' help='--retain_long_orfs &lt; int &gt; ; Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding (default: 900 bp => 300aa)' />
	 </when>
 </conditional>


 <!-- Pfam Options -->

 <conditional name='pfam'>
	<param name='options' type='select' label='Use Pfam Options [ Optional ]'>
		<option value='no'>NO</option>
		<option value='yes'>YES</option>	
	</param>
	<when value='no'/>
	<when value='yes'>
		<param name='pfam_db' type='select' label='Search pfam database' help=' --search_pfam  &lt; pfam_db.hmm &gt; ; /path/to/pfam_db.hmm to search using hmmscan'>
    			<options from_file="pfam_db.loc">
				<column name="name" index="0"/>
		       	 	<column name="value" index="2"/>
			</options>
		</param>
		<param name='CPU' type='integer' value='2'  label='CPU' help='--CPU &lt; int &gt; Number of CPU for the job'/>
	</when>
  </conditional>

</inputs>
<outputs>
	<data name='transdecoder_pep' format='fasta' label="${tool.name} on ${on_string}: pep" from_work_dir="transcript.transdecoder.pep"/>
	<data name='transdecoder_cds' format='fasta' label="${tool.name} on ${on_string}: cds" from_work_dir="transcript.transdecoder.cds"/>
	<data name='transdecoder_bed' format='bed' label="${tool.name} on ${on_string}: bed" from_work_dir="transcript.transdecoder.bed"/>
	<data name='transdecoder_gff3' format='tabular' label="${tool.name} on ${on_string}: gff3" from_work_dir="transcript.transdecoder.gff3"/>
	<data name='transdecoder_mRNA' format='fasta' label="${tool.name} on ${on_string}: mRNA" from_work_dir="transcript.transdecoder.mRNA"/>
	<data name='transdecoder_log' format='txt' label="${tool.name} on ${on_string}: log" />
</outputs>
</tool>