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annotate transdecoder.xml @ 5:c6334cb383ff draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
author iuc
date Thu, 08 Oct 2020 12:33:46 +0000
parents 0db979fead3a
children d0d4cef4f967
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5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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1 <tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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2 <description>finds coding regions within transcripts</description>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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3 <macros>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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4 <token name="@TOOL_VERSION@">5.5.0</token>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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5 <token name="@VERSION_SUFFIX@">0</token>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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6 </macros>
0
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement>
0
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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9 </requirements>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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10 <version_command><![CDATA[TransDecoder.LongOrfs --version 2>&1 | grep 'TransDecoder.LongOrfs' | cut -f 2 -d ' ']]></version_command>
4
0db979fead3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit f0e5f4748034bc0f1faafcec65bffa34b64a4781
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11 <command detect_errors="exit_code"><![CDATA[
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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12 ## initialize
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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13 ln -s '${t}' 'transcripts.fasta' &&
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14
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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15 ## run TransDecoder.LongOrfs
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16 TransDecoder.LongOrfs
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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17 ## Shared options
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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18 -t 'transcripts.fasta'
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19 -G '${G}'
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20 ## LongOrfs options
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21 #if $lo.gene_trans_map
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22 --gene_trans_map '${lo.gene_trans_map}'
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23 #end if
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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24 -m $lo.m
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25 ${lo.S}
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26 -O 'output' ## required, otherwise value of -t is used as output folder
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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27
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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28 ## run TransDecoder.Predict
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29 #if $po.predict_cond.predict_sel == 'yes'
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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30 && TransDecoder.Predict
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31 ## Shared options
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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32 -t 'transcripts.fasta'
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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33 -G '${G}'
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34 ## Predict options
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35 --retain_long_orfs_mode $po.predict_cond.mode_cond.mode_sel
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36 #if $po.predict_cond.mode_cond.mode_sel == 'strict'
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37 --retain_long_orfs_length $po.predict_cond.mode_cond.retain_long_orfs_length
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38 #end if
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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39 #if $po.predict_cond.retain_pfam_hits
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40 --retain_pfam_hits '$po.predict_cond.retain_pfam_hits'
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41 #end if
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42 #if $po.predict_cond.retain_blastp_hits
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43 --retain_blastp_hits '$po.predict_cond.retain_blastp_hits'
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44 #end if
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45 $po.predict_cond.single_best_only
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46 $po.predict_cond.no_refine_starts
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47 -T $po.predict_cond.T
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48 -O 'output'
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49 #end if
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50
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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51 ## postprocessing
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52 #if 'log' in $oo.out
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53 |& tee '$out_log'
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54 #end if
0
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55 ]]></command>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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56 <inputs>
5
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57 <param argument="-t" type="data" format="fasta" label="Select file with transcripts"/>
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58 <param argument="-G" type="select" label="Select genetic code">
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59 <option value="Acetabularia">Acetabularia</option>
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60 <option value="Candida">Candida</option>
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61 <option value="Ciliate">Ciliate</option>
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62 <option value="Dasycladacean">Dasycladacean</option>
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63 <option value="Euplotid">Euplotid</option>
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64 <option value="Hexamita">Hexamita</option>
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65 <option value="Mesodinium">Mesodinium</option>
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66 <option value="Mitochondrial-Ascidian">Mitochondrial-Ascidian</option>
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67 <option value="Mitochondrial-Chlorophycean">Mitochondrial-Chlorophycean</option>
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68 <option value="Mitochondrial-Echinoderm">Mitochondrial-Echinoderm</option>
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69 <option value="Mitochondrial-Flatworm">Mitochondrial-Flatworm</option>
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70 <option value="Mitochondrial-Invertebrates">Mitochondrial-Invertebrates</option>
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71 <option value="Mitochondrial-Protozoan">Mitochondrial-Protozoan</option>
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72 <option value="Mitochondrial-Pterobranchia">Mitochondrial-Pterobranchia</option>
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73 <option value="Mitochondrial-Scenedesmus_obliquus">Mitochondrial-Scenedesmus_obliquus</option>
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74 <option value="Mitochondrial-Thraustochytrium">Mitochondrial-Thraustochytrium</option>
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75 <option value="Mitochondrial-Trematode">Mitochondrial-Trematode</option>
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76 <option value="Mitochondrial-Vertebrates">Mitochondrial-Vertebrates</option>
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77 <option value="Mitochondrial-Yeast">Mitochondrial-Yeast</option>
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78 <option value="Pachysolen_tannophilus">Pachysolen_tannophilus</option>
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79 <option value="Peritrich">Peritrich</option>
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80 <option value="SR1_Gracilibacteria">SR1_Gracilibacteria</option>
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81 <option value="Tetrahymena">Tetrahymena</option>
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82 <option value="Universal" selected="true">Universal</option>
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83 </param>
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84 <section name="lo" title="LongOrfs options" expanded="true">
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85 <param argument="--gene_trans_map" type="data" format="tabular" optional="true" label="Select gene-to-transcript identifier mapping file" help="gene_id&lt;tab&gt;trans_id&lt;return&gt;"/>
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86 <param argument="-m" type="integer" value="100" min="1" label="Set minimum protein length"/>
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87 <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Activate strand-specificity?" help="Only analyse top strand."/>
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88 </section>
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89 <section name="po" title="Predict options" expanded="true">
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90 <!--
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91 TransDecoder.Predict can be skipped if only longest_orfs.pep (as a result of TransDecoder.LongOrfs) is required, e.g. for homology search via BlastP and Pfam.
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92 -->
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93 <conditional name="predict_cond">
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94 <param name="predict_sel" type="select" label="Should likely coding regions be predicted?" help="(TransDecoder.Predict)">
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95 <option value="yes" selected="true">Yes</option>
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96 <option value="no">No</option>
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97 </param>
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98 <when value="yes">
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99 <conditional name="mode_cond">
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100 <param argument="mode_sel" type="select" label="Select mode to retain long ORFs" help="In dynamic mode: set range according to 1% FDR in a random sequence of same GC content.">
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101 <option value="dynamic" selected="true">Dynamic</option>
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102 <option value="strict">Strict</option>
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103 </param>
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104 <when value="dynamic"/>
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105 <when value="strict">
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106 <param argument="--retain_long_orfs_length" type="integer" value="1000000" min="0" label="Set long ORFs length" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding."/>
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107 </when>
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108 </conditional>
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109 <param argument="--retain_blastp_hits" type="data" format="tabular" optional="true" label="Select BlastP result file" help="Any ORF with a blast match will be retained in the final output. (outfmt 6 format)"/>
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110 <param argument="--retain_pfam_hits" type="data" format="tabular" optional="true" label="Select Pfam result file" help="Domain table output file from running hmmscan to search Pfam. Any ORF with a pfam domain hit will be retained in the final output. (domtblout file)"/>
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111 <param argument="--single_best_only" type="boolean" truevalue="--single_best_only" falsevalue="" label="Retain only the single best ORF per transcript?" help="Prioritized by homology than ORF length."/>
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112 <param argument="--no_refine_starts" type="boolean" truevalue="--no_refine_starts" falsevalue="" label="Start refinement that identifies potential start codons for 5' partial ORFs using a PWM?"/>
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113 <param argument="-T" type="integer" value="500" min="1" label="Set top longest ORFs to train Markov Model" help="The first (10*value) elements are selected for removing redundancies. Then number of longst ORFs of this value are selected from the non-redundant set."/>
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114 </when>
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115 <when value="no"/>
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116 </conditional>
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117 </section>
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118 <section name="oo" title="Output options">
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119 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Only shown in history if selected here and generated by the specific NOVOplasty run.">
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120 <!-- LongOrfs -->
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121 <option value="lo_cds">Longest ORFs (CDS)</option>
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122 <option value="lo_gff3">Longest ORFs (GFF3)</option>
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123 <option value="lo_pep" selected="true">Longest ORFs (PEP)</option>
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124 <!-- Predict -->
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125 <option value="bed" selected="true">Results (BED)</option>
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126 <option value="cds" selected="true">Results (CDS)</option>
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127 <option value="gff3" selected="true">Results (GFF3)</option>
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128 <option value="pep" selected="true">Results (PEP)</option>
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129 <!-- Others -->
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130 <option value="log">Log</option>
0
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131 </param>
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132 </section>
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133 </inputs>
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134 <outputs>
5
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135 <!-- LongOrfs -->
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136 <data name="out_lo_cds" format="fasta" from_work_dir="output/longest_orfs.cds" label="${tool.name} on ${on_string}: Longest ORFs (CDS/FASTA)">
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137 <filter>'lo_cds' in oo['out']</filter>
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138 </data>
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139 <data name="out_lo_gff3" format="gff3" from_work_dir="output/longest_orfs.gff3" label="${tool.name} on ${on_string}: Longest ORFs (GFF3)">
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140 <filter>'lo_gff3' in oo['out']</filter>
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141 </data>
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142 <data name="out_lo_pep" format="fasta" from_work_dir="output/longest_orfs.pep" label="${tool.name} on ${on_string}: Longest ORFs (PEP/FASTA)">
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143 <filter>'lo_pep' in oo['out']</filter>
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144 </data>
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145 <!-- Predict -->
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146 <data name="out_bed" format="bed" from_work_dir="transcripts.fasta.transdecoder.bed" label="${tool.name} on ${on_string}: Results (BED)">
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147 <filter>'bed' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter>
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148 </data>
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149 <data name="out_cds" format="fasta" from_work_dir="transcripts.fasta.transdecoder.cds" label="${tool.name} on ${on_string}: Results (CDS/FASTA)">
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150 <filter>'cds' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter>
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151 </data>
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152 <data name="out_gff3" format="gff3" from_work_dir="transcripts.fasta.transdecoder.gff3" label="${tool.name} on ${on_string}: Results (GFF3)">
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153 <filter>'gff3' in oo['out'] and po['predict_cond']['predict_sel'] =='yes'</filter>
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154 </data>
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155 <data name="out_pep" format="fasta" from_work_dir="transcripts.fasta.transdecoder.pep" label="${tool.name} on ${on_string}: Results (PEP/FASTA)">
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156 <filter>'pep' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter>
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157 </data>
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158 <!-- Others -->
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159 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
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160 <filter>'log' in oo['out']</filter>
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161 </data>
0
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162 </outputs>
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163 <tests>
5
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164 <!-- no test implemented for: gene_trans_map, retain_blastp_hits, retain_pfam_hits -->
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165
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diff changeset
166 <!-- #1 default -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
167 <test expect_num_outputs="5">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
168 <param name="t" value="transcripts.fasta"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
169 <!-- LongOrfs -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
170 <output name="out_lo_pep">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
171 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
172 <has_n_lines n="772"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
173 <has_text_matching expression=".+comp874.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
174 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
175 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
176 <!-- Predict -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
177 <output name="out_bed">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
178 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
179 <has_n_lines n="337"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
180 <has_text_matching expression="comp98\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
181 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
182 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
183 <output name="out_cds">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
184 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
185 <has_n_lines n="6959"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
186 <has_text_matching expression=">comp98\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
187 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
188 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
189 <output name="out_gff3">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
190 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
191 <has_n_lines n="2165"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
192 <has_text_matching expression="comp98\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
193 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
194 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
195 <output name="out_pep">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
196 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
197 <has_n_lines n="2644"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
198 <has_text_matching expression="comp98\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
199 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
200 </output>
0
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
201 </test>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
202 <!-- #2 -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
203 <test expect_num_outputs="8">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
204 <param name="t" value="transcripts.fasta"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
205 <param name="G" value="Acetabularia"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
206 <section name="lo">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
207 <param name="m" value="101"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
208 <param name="S" value="true"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
209 </section>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
210 <section name="po">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
211 <conditional name="predict_cond">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
212 <param name="predict_sel" value="yes"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
213 <conditional name="mode_cond">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
214 <param name="mode_sel" value="dynamic"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
215 </conditional>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
216 <param name="single_best_only" value="true"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
217 <param name="no_refine_starts" value="true"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
218 <param name="T" value="501"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
219 </conditional>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
220 </section>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
221 <section name="oo">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
222 <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,log"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
223 </section>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
224 <!-- LongOrfs -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
225 <output name="out_lo_cds">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
226 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
227 <has_n_lines n="1454"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
228 <has_text_matching expression=">comp874\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
229 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
230 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
231 <output name="out_lo_gff3">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
232 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
233 <has_n_lines n="4565"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
234 <has_text_matching expression="comp874\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
235 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
236 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
237 <output name="out_lo_pep">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
238 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
239 <has_n_lines n="1454"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
240 <has_text_matching expression=">comp874\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
241 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
242 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
243 <!-- Predict -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
244 <output name="out_bed">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
245 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
246 <has_n_lines n="340"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
247 <has_text_matching expression="comp98\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
248 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
249 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
250 <output name="out_cds">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
251 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
252 <has_n_lines n="7512"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
253 <has_text_matching expression=">comp98\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
254 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
255 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
256 <output name="out_gff3">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
257 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
258 <has_n_lines n="2000"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
259 <has_text_matching expression="comp98\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
260 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
261 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
262 <output name="out_pep">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
263 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
264 <has_n_lines n="2833"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
265 <has_text_matching expression=">comp98\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
266 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
267 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
268 <!-- Others -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
269 <output name="out_log">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
270 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
271 <has_text_matching expression="transdecoder is finished.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
272 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
273 </output>
0
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
274 </test>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
275 <!-- #3 -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
276 <test expect_num_outputs="8">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
277 <param name="t" value="transcripts.fasta"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
278 <section name="po">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
279 <conditional name="predict_cond">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
280 <param name="predict_sel" value="yes"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
281 <conditional name="mode_cond">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
282 <param name="mode_sel" value="strict"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
283 <param name="retain_long_orfs_length" value="1000001"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
284 </conditional>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
285 </conditional>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
286 </section>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
287 <section name="oo">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
288 <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,log"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
289 </section>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
290 <!-- LongOrfs -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
291 <output name="out_lo_cds">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
292 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
293 <has_n_lines n="772"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
294 <has_text_matching expression=">comp874\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
295 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
296 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
297 <output name="out_lo_gff3">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
298 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
299 <has_n_lines n="2486"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
300 <has_text_matching expression="comp874\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
301 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
302 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
303 <output name="out_lo_pep">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
304 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
305 <has_n_lines n="772"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
306 <has_text_matching expression=">comp874\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
307 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
308 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
309 <!-- Predict -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
310 <output name="out_bed">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
311 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
312 <has_n_lines n="337"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
313 <has_text_matching expression="comp98\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
314 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
315 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
316 <output name="out_cds">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
317 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
318 <has_n_lines n="6959"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
319 <has_text_matching expression=">comp98\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
320 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
321 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
322 <output name="out_gff3">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
323 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
324 <has_n_lines n="2165"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
325 <has_text_matching expression="comp98\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
326 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
327 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
328 <output name="out_pep">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
329 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
330 <has_n_lines n="2644"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
331 <has_text_matching expression=">comp98\_c0\_seq1.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
332 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
333 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
334 <!-- Others -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
335 <output name="out_log">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
336 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
337 <has_text_matching expression="transdecoder is finished.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
338 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
339 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
340 </test>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
341 <!-- #4 -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
342 <test expect_num_outputs="1">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
343 <param name="t" value="transcripts.fasta"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
344 <section name="po">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
345 <conditional name="predict_cond">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
346 <param name="predict_sel" value="no"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
347 </conditional>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
348 </section>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
349 <!-- LongOrfs -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
350 <output name="out_lo_pep">
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351 <assert_contents>
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352 <has_n_lines n="772"/>
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353 <has_text_matching expression="c"/>
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354 </assert_contents>
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355 </output>
0
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356 </test>
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357 </tests>
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358 <help><![CDATA[
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359 .. class:: infomark
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360
0
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361 **What it does**
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362
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363 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.
0
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364
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365 TransDecoder identifies likely coding sequences based on the following criteria:
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366
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367 - a minimum length open reading frame (ORF) is found in a transcript sequence.
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368 - a log-likelihood score similar to what is computed by the GeneID software is > 0.
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369 - 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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370 - 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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371 - a PSSM is built/trained/used to refine the start codon prediction.
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372 - optional the putative peptide has a match to a Pfam domain above the noise cutoff score.
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373
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374 *Step 1*: Extract long open reading frames
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375
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376 By default, TransDecoder.LongOrfs will identify ORFs that are at least 100 amino acids long. You can lower this via the '-m' parameter, but know that the rate of false positive ORF predictions increases drastically with shorter minimum length criteria.
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377
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378 *Step 2*: (optional and not part of this wrapper)
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379
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380 The result "longest ORFs (PEP)" can be used to identify ORFs with homology to known proteins via BlastP or Pfam searches (`details <https://github.com/TransDecoder/TransDecoder/wiki#including-homology-searches-as-orf-retention-criteria>`_).
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381
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382 *Step 3*: Predict the likely coding regions
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383
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384 Optionally apply results of homology searches in this step and re-run the whole analysis.
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385
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386 **Input**
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387
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388 - FASTA file with transcripts
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389 - (optional) gene-to-transcript identifier mapping file
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390 - (optional) BLAST or Pfam database file (`details <https://github.com/TransDecoder/TransDecoder/wiki#including-homology-searches-as-orf-retention-criteria>`_)
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391
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392 **Output**
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393
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394 *LongOrfs*
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395
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396 - longest ORFs (PEP/FASTA): all ORFs meeting the minimum length criteria, regardless of coding potential
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397 - longest ORFs (GFF3): positions of all ORFs as found in the target transcripts
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398 - longest ORFs (CDS/FASTA): the nucleotide coding sequence for all detected ORFs
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399
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400 *Predict*
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401
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402 - Results (PEP/FASTA): peptide sequences for the final candidate ORFs; all shorter candidates within longer ORFs were removed
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403 - Results (CDS/FASTA): nucleotide sequences for coding regions of the final candidate ORFs
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404 - Results (GFF3): positions within the target transcripts of the final selected ORFs
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405 - Results (BED): BED-formatted file describing ORF positions, best for viewing using GenomeView or IGV
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406
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407 *Other*
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408
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409 - Log file
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410
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411 .. class:: infomark
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412
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413 **References**
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414
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415 More information are available on `GitHub <https://github.com/TransDecoder/TransDecoder>`_.
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416 ]]></help>
4
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417 <citations>
0
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418 <citation type="doi">10.1038/nprot.2013.084</citation>
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419 </citations>
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420 </tool>