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1 <tool id='id_transDecoder' name='transDecoder' version='1.0'>
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2 <description> coding region </description>
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3 <!--requirement></requirement-->
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4 <requirements>
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5 <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
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6 <requirement type="set_environment">TRINITY_HOME</requirement>
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7
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8 </requirements>
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9 <command>perl \$TRINITY_HOME/trinity-plugins/transdecoder/TransDecoder
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10
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11 -t $transcript
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12
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13 #if str($optional.parameters) == 'yes':
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14 #if ($train):
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15 --train $train
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16 #end if
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17
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18 #if ($min_protein_length):
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19 -m $min_protein_length
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20 #end if
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21
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22 #if ($genetic_code):
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23 -G $genetic_code
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24 #end if
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25
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26 #if ($strand-specific):
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27 $strand-specific
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28 #end if
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29
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30 #if ($lottmn):
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31 -T $lottmm
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32 #end if
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33
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34 #if ($retain_long_orfs):
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35 --retain_long_orfs $retain_long_orfs
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36 #end if
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37 #end if
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38
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39 #if str($pfam.options) == 'yes':
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40 #if ($pfam_db):
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41 --search_pfam $pfam_db
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42 #end if
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43
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44 #if ($CPU):
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45 --CPU $CPU
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46 #end if
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47 #end if
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48
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49 ##log file
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50 > $transdecoder_log 2>&1;
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51
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52
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53 ## output renaming
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54
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55 cp -s dataset_*.dat.transdecoder.pep transcript.transdecoder.pep;
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56 cp -s dataset_*.dat.transdecoder.cds transcript.transdecoder.cds;
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57 cp -s dataset_*.dat.transdecoder.bed transcript.transdecoder.bed;
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58 cp -s dataset_*.dat.transdecoder.gff3 transcript.transdecoder.gff3;
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59 cp -s dataset_*.dat.transdecoder.mRNA transcript.transdecoder.mRNA;
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60 </command>
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61
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62 <inputs>
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63 <!-- Required -->
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64
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65 <param name='transcript' type='data' label='Transcripts [ in fasta format ]' help=' -t < string > ; Assembled reads in fasta file format'/>
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66
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67 <!-- Optional -->
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68
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69 <conditional name='optional'>
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70 <param name='parameters' type='select' label='Use Optional Parameters'>
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71 <option value='no'>NO</option>
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72 <option value='yes'>YES</option>
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73 </param>
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74 <when value='no'/>
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75 <when value='yes'>
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76 <param name='train' type='data' optional='true' label='FASTA file with ORFs to train Markov Mod for protein identification' help='--train < string > ; FASTA file with ORFs to train Markov Mod for protein identification; otherwise longest non-redundant ORFs used' />
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77 <param name='min_protein_length' type='integer' optional='true' value='100' label='Minimum Protein Length' help='-m < int > ;minimum protein length (default: 100)'/>
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78 <param name='genetic_code' type='select' optional='true' label='Select Genetic Code' help=' -G < string > ; genetic code (default is "universal")'>
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79 <option value='universal' selected='true'>Universal</option>
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80 <option value='Euplotes'>Euplotes</option>
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81 <option value='Tetrahymena'>Tetrahymena</option>
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82 <option value='Candida'>Candida</option>
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83 <option value='Acetabularia'>Acetabularia</option>
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84 </param>
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85 <param name='strand-specific' type='boolean' truevalue='-S' falsevalue='' optional='true' label='Strand-Specific [ -S ]' help='strand-specific (only analyzes top strand)'/>
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86 <param name='lottmm' type='integer' optional='true' value='500' label=' -T ; Needs a label ??? ' help='-T < int > ; If no --train, top longest ORFs to train Markov Model (hexamer stats) (default: 500)'/>
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87 <param name='retain_long_orfs' type="integer" optional='true' value="900" label=' --retain_long_orfs ; Needs a label ??? ' help='--retain_long_orfs < int > ; 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)' />
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88 </when>
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89 </conditional>
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90
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91
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92 <!-- Pfam Options -->
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93
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94 <conditional name='pfam'>
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95 <param name='options' type='select' label='Use Pfam Options [ Optional ]'>
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96 <option value='no'>NO</option>
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97 <option value='yes'>YES</option>
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98 </param>
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99 <when value='no'/>
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100 <when value='yes'>
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101 <param name='pfam_db' type='select' label='Search pfam database' help=' --search_pfam < pfam_db.hmm > ; /path/to/pfam_db.hmm to search using hmmscan'>
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102 <options from_file="pfam_db.loc">
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103 <column name="name" index="0"/>
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104 <column name="value" index="2"/>
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105 </options>
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106 </param>
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107 <param name='CPU' type='integer' value='2' label='CPU' help='--CPU < int > Number of CPU for the job'/>
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108 </when>
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109 </conditional>
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110
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111 </inputs>
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112 <outputs>
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113 <data name='transdecoder_pep' format='fasta' label="${tool.name} on ${on_string}: pep" from_work_dir="transcript.transdecoder.pep"/>
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114 <data name='transdecoder_cds' format='fasta' label="${tool.name} on ${on_string}: cds" from_work_dir="transcript.transdecoder.cds"/>
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115 <data name='transdecoder_bed' format='bed' label="${tool.name} on ${on_string}: bed" from_work_dir="transcript.transdecoder.bed"/>
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116 <data name='transdecoder_gff3' format='tabular' label="${tool.name} on ${on_string}: gff3" from_work_dir="transcript.transdecoder.gff3"/>
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117 <data name='transdecoder_mRNA' format='fasta' label="${tool.name} on ${on_string}: mRNA" from_work_dir="transcript.transdecoder.mRNA"/>
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118 <data name='transdecoder_log' format='txt' label="${tool.name} on ${on_string}: log" />
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119 </outputs>
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120 </tool>
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