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annotate transdecoder.xml @ 0:57129de238f3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
author iuc
date Fri, 20 Nov 2015 06:46:29 -0500
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57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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1 <tool id="transdecoder" name="TransDecoder" version="1.0">
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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2 <description>Find coding regions within transcripts</description>
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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3 <requirements>
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4 <requirement type="package" version="2.0.1">transdecoder</requirement>
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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5 </requirements>
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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7 <stdio>
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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8 <exit_code range="1:" level="fatal" description="Error occurred" />
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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9 </stdio>
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10
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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11 <command><![CDATA[
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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12 TransDecoder.LongOrfs -t "${input}"
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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13
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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14 #if ($min_len):
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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15 -m ${min_len}
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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16 #end if
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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18 ${adv.stranded}
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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20 #if ($adv.gen_code):
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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21 -G ${adv.gen_code}
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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22 #end if
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24 &&
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26 TransDecoder.Predict -t "${input}"
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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28 #if ($adv.retain_long_orfs):
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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29 --retain_long_orfs ${adv.retain_long_orfs}
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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30 #end if
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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31
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32 #if str( $training_sect.training.training_selector ) == "training_top":
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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33 #if ($training_sect.training.top_longest):
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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34 -T ${training_sect.training.top_longest}
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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35 #end if
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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36 #else
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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37 #if ($training_sect.training.train):
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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38 --train ${training_sect.training.train}
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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39 #end if
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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40 #end if
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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41
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42 &&
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57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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44 out_prefix=`basename "${input}"`
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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45
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46 mv `basename "${input}"`.transdecoder.pep transcript.transdecoder.pep &&
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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47 mv `basename "${input}"`.transdecoder.cds transcript.transdecoder.cds &&
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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48 mv `basename "${input}"`.transdecoder.bed transcript.transdecoder.bed &&
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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49 mv `basename "${input}"`.transdecoder.gff3 transcript.transdecoder.gff3 &&
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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50 mv `basename "${input}"`.transdecoder.mRNA transcript.transdecoder.mRNA
57129de238f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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51 ]]></command>
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52
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53 <inputs>
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54 <param format="fasta" name="input" type="data" label="Transcripts"/>
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55
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56 <param name="min_len" size="5" type="integer" optional='true' value="100" label="Minimum protein length (default: 100aa)"/>
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57
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58 <section name="adv" title="Advanced Options" expanded="False">
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59 <param name="stranded" type="boolean" checked="false" truevalue="-S" falsevalue="" label="Strand-specific" help="Only analyzes top strand"/>
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60 <param name="gen_code" type="select" label="Genetic code">
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61 <option value="universal" selected="True">universal</option>
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62 <option value="Euplotes">Euplotes</option>
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63 <option value="Tetrahymena">Tetrahymena</option>
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64 <option value="Candida">Candida</option>
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65 <option value="Acetabularia">Acetabularia</option>
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66 <option value="Mitochondrial-Canonical">Mitochondrial-Canonical</option>
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67 <option value="Mitochondrial-Vertebrates">Mitochondrial-Vertebrates</option>
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68 <option value="Mitochondrial-Arthropods">Mitochondrial-Arthropods</option>
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69 <option value="Mitochondrial-Echinoderms">Mitochondrial-Echinoderms</option>
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70 <option value="Mitochondrial-Molluscs">Mitochondrial-Molluscs</option>
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71 <option value="Mitochondrial-Ascidians">Mitochondrial-Ascidians</option>
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72 <option value="Mitochondrial-Nematodes">Mitochondrial-Nematodes</option>
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73 <option value="Mitochondrial-Platyhelminths">Mitochondrial-Platyhelminths</option>
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74 <option value="Mitochondrial-Yeasts">Mitochondrial-Yeasts</option>
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75 <option value="Mitochondrial-Euascomycetes">Mitochondrial-Euascomycetes</option>
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76 <option value="Mitochondrial-Protozoans">Mitochondrial-Protozoans</option>
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77 </param>
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78
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79 <param name="retain_long_orfs" type="integer" optional="true" label="Retain long orfs" help="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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80 </section>
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81
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82 <section name="training_sect" title="Training Options" expanded="False">
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83 <conditional name="training">
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84 <param name="training_selector" type="select" label="Select the training method">
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85 <option value="training_top" selected="True">Train with the top longest ORFs</option>
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86 <option value="training_set">Train with a set of known ORFs</option>
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87 </param>
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88 <when value="training_top">
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89 <param name="top_longest" type="integer" optional="true" label="Number of top longest ORFs" help="Number of top longest ORFs to train Markov Model (hexamer stats) (default: 500 sequences)" />
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90 </when>
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91 <when value="training_set">
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92 <param format="fasta" name="train" type="data" label="Training set of transcripts" optional="true" help="FASTA file with ORFs to train Markov Mod for protein identification" />
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93 </when>
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94 </conditional>
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95 </section>
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96
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97 </inputs>
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98
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99
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100 <outputs>
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101 <data name='transdecoder_pep' format='fasta' label="${tool.name} on ${on_string}: pep" from_work_dir="transcript.transdecoder.pep"/>
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102 <data name='transdecoder_cds' format='fasta' label="${tool.name} on ${on_string}: cds" from_work_dir="transcript.transdecoder.cds"/>
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103 <data name='transdecoder_bed' format='bed' label="${tool.name} on ${on_string}: bed" from_work_dir="transcript.transdecoder.bed"/>
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104 <data name='transdecoder_gff3' format='gff3' label="${tool.name} on ${on_string}: gff3" from_work_dir="transcript.transdecoder.gff3"/>
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105 <data name='transdecoder_mRNA' format='fasta' label="${tool.name} on ${on_string}: mRNA" from_work_dir="transcript.transdecoder.mRNA"/>
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106 </outputs>
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107
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108
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109 <tests>
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110 <test>
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111 <param name="input" value="test.fa"/>
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112 <output name="transdecoder_gff3" file="raw/test.fa.transdecoder.gff3" compare="sim_size" />
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113 <output name="transdecoder_bed" file="raw/test.fa.transdecoder.bed" compare="sim_size" />
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114 <output name="transdecoder_cds" file="raw/test.fa.transdecoder.cds" compare="sim_size" />
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115 <output name="transdecoder_mRNA" file="raw/test.fa.transdecoder.mRNA" compare="sim_size" />
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116 <output name="transdecoder_pep" file="raw/test.fa.transdecoder.pep" compare="sim_size" />
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117 </test>
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118 <test>
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119 <param name="input" value="test.fa"/>
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120 <param name="training_selector" value="training_top"/>
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121 <param name="top_longest" value="10"/>
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122 <output name="transdecoder_gff3" file="top/test.fa.transdecoder.gff3" compare="sim_size" />
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123 <output name="transdecoder_bed" file="top/test.fa.transdecoder.bed" compare="sim_size" />
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124 <output name="transdecoder_cds" file="top/test.fa.transdecoder.cds" compare="sim_size" />
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125 <output name="transdecoder_mRNA" file="top/test.fa.transdecoder.mRNA" compare="sim_size" />
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126 <output name="transdecoder_pep" file="top/test.fa.transdecoder.pep" compare="sim_size" />
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127 </test>
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128 <test>
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129 <param name="input" value="test.fa"/>
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130 <param name="gen_code" value="Mitochondrial-Arthropods"/>
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131 <output name="transdecoder_gff3" file="gencode/test.fa.transdecoder.gff3" compare="sim_size" />
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132 <output name="transdecoder_bed" file="gencode/test.fa.transdecoder.bed" compare="sim_size" />
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133 <output name="transdecoder_cds" file="gencode/test.fa.transdecoder.cds" compare="sim_size" />
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134 <output name="transdecoder_mRNA" file="gencode/test.fa.transdecoder.mRNA" compare="sim_size" />
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135 <output name="transdecoder_pep" file="gencode/test.fa.transdecoder.pep" compare="sim_size" />
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136 </test>
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137 <test>
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138 <param name="input" value="test.fa"/>
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139 <param name="stranded" value="true"/>
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140 <output name="transdecoder_gff3" file="strand/test.fa.transdecoder.gff3" compare="sim_size" />
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141 <output name="transdecoder_bed" file="strand/test.fa.transdecoder.bed" compare="sim_size" />
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142 <output name="transdecoder_cds" file="strand/test.fa.transdecoder.cds" compare="sim_size" />
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143 <output name="transdecoder_mRNA" file="strand/test.fa.transdecoder.mRNA" compare="sim_size" />
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144 <output name="transdecoder_pep" file="strand/test.fa.transdecoder.pep" compare="sim_size" />
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145 </test>
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146 </tests>
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147 <help>
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148
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149 **What it does**
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150
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151 TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
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152
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153 TransDecoder identifies likely coding sequences based on the following criteria:
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154
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155 - a minimum length open reading frame (ORF) is found in a transcript sequence
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156
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157 - a log-likelihood score similar to what is computed by the GeneID software is > 0.
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158
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159 - the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames.
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160
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161 - if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc).
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162
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163 - optional the putative peptide has a match to a Pfam domain above the noise cutoff score.
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164
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165 The software is primarily maintained by Brian Haas at the Broad Institute and Alexie Papanicolaou at the Commonwealth Scientific and Industrial Research Organisation (CSIRO). It is integrated into other related software such as Trinity, PASA, EVidenceModeler, and Trinotate.
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166
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167 </help>
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168 <citations>
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169 <citation type="doi">10.1038/nprot.2013.084</citation>
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170 </citations>
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171 </tool>