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annotate transdecoder.xml @ 7:ffd1300599a1 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 2147ee46c226f99d16899eb29b223f0f80db5491"
author iuc
date Fri, 22 Oct 2021 11:15:03 +0000
parents d0d4cef4f967
children
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ffd1300599a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 2147ee46c226f99d16899eb29b223f0f80db5491"
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1 <tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>finds coding regions within transcripts</description>
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3 <xrefs>
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4 <xref type="bio.tools">TransDecoder</xref>
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5 </xrefs>
5
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6 <macros>
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7 <token name="@TOOL_VERSION@">5.5.0</token>
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8 <token name="@VERSION_SUFFIX@">2</token>
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9 </macros>
0
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement>
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12 <requirement type="package" version="3.0">zip</requirement>
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8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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13 </requirements>
5
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14 <version_command><![CDATA[TransDecoder.LongOrfs --version 2>&1 | grep 'TransDecoder.LongOrfs' | cut -f 2 -d ' ']]></version_command>
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0db979fead3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit f0e5f4748034bc0f1faafcec65bffa34b64a4781
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15 <command detect_errors="exit_code"><![CDATA[
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16 ## initialize
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17 ln -s '${t}' 'transcripts.fasta' &&
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19 ## run TransDecoder.LongOrfs
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20 TransDecoder.LongOrfs
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21 ## Shared options
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22 -t 'transcripts.fasta'
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23 -G '${G}'
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24 ## LongOrfs options
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25 #if $lo.gene_trans_map
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26 --gene_trans_map '${lo.gene_trans_map}'
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27 #end if
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28 -m $lo.m
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29 ${lo.S}
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30 -O 'output' ## required, otherwise value of -t is used as output folder
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31
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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32 ## run TransDecoder.Predict
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33 #if $po.predict_cond.predict_sel == 'yes'
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34 && TransDecoder.Predict
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35 ## Shared options
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36 -t 'transcripts.fasta'
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37 -G '${G}'
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38 ## Predict options
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39 --retain_long_orfs_mode $po.predict_cond.mode_cond.mode_sel
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40 #if $po.predict_cond.mode_cond.mode_sel == 'strict'
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41 --retain_long_orfs_length $po.predict_cond.mode_cond.retain_long_orfs_length
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42 #end if
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43 #if $po.predict_cond.retain_pfam_hits
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44 --retain_pfam_hits '$po.predict_cond.retain_pfam_hits'
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45 #end if
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46 #if $po.predict_cond.retain_blastp_hits
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47 --retain_blastp_hits '$po.predict_cond.retain_blastp_hits'
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48 #end if
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49 $po.predict_cond.single_best_only
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50 $po.predict_cond.no_refine_starts
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51 -T $po.predict_cond.T
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52 -O 'output'
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53 #end if
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54
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55 ## postprocessing
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56 #if 'log' in $oo.out
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57 |& tee '$out_log'
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58 #end if
6
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59 && if ls 'output/'*'.pdf' >/dev/null 2>&1; then zip 'seqlogo.zip' 'output/'*'.pdf' -q -j; fi
0
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60 ]]></command>
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61 <inputs>
5
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62 <param argument="-t" type="data" format="fasta" label="Select file with transcripts"/>
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63 <param argument="-G" type="select" label="Select genetic code">
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64 <option value="Acetabularia">Acetabularia</option>
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65 <option value="Candida">Candida</option>
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66 <option value="Ciliate">Ciliate</option>
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67 <option value="Dasycladacean">Dasycladacean</option>
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68 <option value="Euplotid">Euplotid</option>
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69 <option value="Hexamita">Hexamita</option>
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70 <option value="Mesodinium">Mesodinium</option>
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71 <option value="Mitochondrial-Ascidian">Mitochondrial-Ascidian</option>
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72 <option value="Mitochondrial-Chlorophycean">Mitochondrial-Chlorophycean</option>
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73 <option value="Mitochondrial-Echinoderm">Mitochondrial-Echinoderm</option>
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74 <option value="Mitochondrial-Flatworm">Mitochondrial-Flatworm</option>
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75 <option value="Mitochondrial-Invertebrates">Mitochondrial-Invertebrates</option>
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76 <option value="Mitochondrial-Protozoan">Mitochondrial-Protozoan</option>
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77 <option value="Mitochondrial-Pterobranchia">Mitochondrial-Pterobranchia</option>
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78 <option value="Mitochondrial-Scenedesmus_obliquus">Mitochondrial-Scenedesmus_obliquus</option>
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79 <option value="Mitochondrial-Thraustochytrium">Mitochondrial-Thraustochytrium</option>
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80 <option value="Mitochondrial-Trematode">Mitochondrial-Trematode</option>
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81 <option value="Mitochondrial-Vertebrates">Mitochondrial-Vertebrates</option>
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82 <option value="Mitochondrial-Yeast">Mitochondrial-Yeast</option>
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83 <option value="Pachysolen_tannophilus">Pachysolen_tannophilus</option>
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84 <option value="Peritrich">Peritrich</option>
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85 <option value="SR1_Gracilibacteria">SR1_Gracilibacteria</option>
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86 <option value="Tetrahymena">Tetrahymena</option>
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87 <option value="Universal" selected="true">Universal</option>
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88 </param>
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89 <section name="lo" title="LongOrfs options" expanded="true">
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90 <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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91 <param argument="-m" type="integer" value="100" min="1" label="Set minimum protein length"/>
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92 <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Activate strand-specificity?" help="Only analyse top strand?"/>
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93 </section>
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94 <section name="po" title="Predict options" expanded="true">
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95 <!--
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96 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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97 -->
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98 <conditional name="predict_cond">
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99 <param name="predict_sel" type="select" label="Should likely coding regions be predicted?" help="(TransDecoder.Predict)">
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100 <option value="yes" selected="true">Yes</option>
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101 <option value="no">No</option>
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102 </param>
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103 <when value="yes">
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104 <conditional name="mode_cond">
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105 <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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106 <option value="dynamic" selected="true">Dynamic</option>
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107 <option value="strict">Strict</option>
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108 </param>
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109 <when value="dynamic"/>
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110 <when value="strict">
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111 <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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112 </when>
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113 </conditional>
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114 <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. (tabular outfmt6 file)"/>
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115 <param argument="--retain_pfam_hits" type="data" format="txt" 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. (tabular domtblout file)"/>
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116 <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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117 <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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118 <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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119 </when>
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120 <when value="no"/>
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121 </conditional>
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122 </section>
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123 <section name="oo" title="Output options" expanded="true">
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124 <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 run.">
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125 <!-- LongOrfs -->
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126 <option value="lo_cds">Longest ORFs (CDS)</option>
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127 <option value="lo_gff3">Longest ORFs (GFF3)</option>
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128 <option value="lo_pep" selected="true">Longest ORFs (PEP)</option>
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129 <!-- Predict -->
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130 <option value="bed" selected="true">Results (BED)</option>
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131 <option value="cds" selected="true">Results (CDS)</option>
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132 <option value="gff3" selected="true">Results (GFF3)</option>
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133 <option value="pep" selected="true">Results (PEP)</option>
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134 <option value="plot">Plots</option>
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135 <!-- Others -->
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136 <option value="log">Log</option>
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137 </param>
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138 </section>
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139 </inputs>
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140 <outputs>
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141 <!-- LongOrfs -->
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142 <data name="out_lo_cds" format="fasta" from_work_dir="output/longest_orfs.cds" label="${tool.name} on ${on_string}: Longest ORFs (CDS/FASTA)">
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143 <filter>'lo_cds' in oo['out']</filter>
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144 </data>
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145 <data name="out_lo_gff3" format="gff3" from_work_dir="output/longest_orfs.gff3" label="${tool.name} on ${on_string}: Longest ORFs (GFF3)">
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146 <filter>'lo_gff3' in oo['out']</filter>
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147 </data>
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148 <data name="out_lo_pep" format="fasta" from_work_dir="output/longest_orfs.pep" label="${tool.name} on ${on_string}: Longest ORFs (PEP/FASTA)">
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149 <filter>'lo_pep' in oo['out']</filter>
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150 </data>
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151 <!-- Predict -->
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152 <data name="out_bed" format="bed" from_work_dir="transcripts.fasta.transdecoder.bed" label="${tool.name} on ${on_string}: Results (BED)">
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153 <filter>'bed' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter>
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154 </data>
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155 <data name="out_cds" format="fasta" from_work_dir="transcripts.fasta.transdecoder.cds" label="${tool.name} on ${on_string}: Results (CDS/FASTA)">
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156 <filter>'cds' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter>
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157 </data>
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158 <data name="out_gff3" format="gff3" from_work_dir="transcripts.fasta.transdecoder.gff3" label="${tool.name} on ${on_string}: Results (GFF3)">
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159 <filter>'gff3' in oo['out'] and po['predict_cond']['predict_sel'] =='yes'</filter>
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160 </data>
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161 <data name="out_pep" format="fasta" from_work_dir="transcripts.fasta.transdecoder.pep" label="${tool.name} on ${on_string}: Results (PEP/FASTA)">
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162 <filter>'pep' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter>
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163 </data>
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164 <data name="out_plot" format="zip" from_work_dir="seqlogo.zip" label="${tool.name} on ${on_string}: Plots">
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165 <filter>'plot' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
166 </data>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
167 <!-- Others -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
168 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
169 <filter>'log' in oo['out']</filter>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
170 </data>
0
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
171 </outputs>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
172 <tests>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
173 <!-- #1 default -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
174 <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
175 <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
176 <!-- LongOrfs -->
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_lo_pep">
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>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
179 <has_n_lines n="190"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
180 <has_line line=">CUFF.20.1.p2 type:3prime_partial len:205 gc:Universal CUFF.20.1:612-1(-)"/>
5
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 <!-- Predict -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
184 <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
185 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
186 <has_n_lines n="81"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
187 <has_text_matching expression="CUFF\.9\.1.+"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
188 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
189 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
190 <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
191 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
192 <has_n_lines n="1578"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
193 <has_line line=">CUFF.9.1.p1 GENE.CUFF.9.1~~CUFF.9.1.p1 ORF type:complete len:156 (+),score=36.30 CUFF.9.1:173-640(+)"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
194 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
195 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
196 <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
197 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
198 <has_n_lines n="542"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
199 <has_text_matching expression="CUFF\.9\.1.+"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
200 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
201 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
202 <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
203 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
204 <has_n_lines n="608"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
205 <has_text_matching expression="CUFF\.9\.1.+"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
206 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
207 </output>
0
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
208 </test>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
209 <!-- #2 -->
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
210 <test expect_num_outputs="9">
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
211 <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
212 <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
213 <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
214 <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
215 <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
216 </section>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
217 <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
218 <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
219 <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
220 <conditional name="mode_cond">
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
221 <param name="mode_sel" value="strict"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
222 <param name="retain_long_orfs_length" value="1000001"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
223 </conditional>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
224 <param name="retain_blastp_hits" value="blastp.outfmt6"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
225 <param name="retain_pfam_hits" value="pfam.domtblout"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
226 <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
227 <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
228 <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
229 </conditional>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
230 </section>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
231 <section name="oo">
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
232 <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,plot,log"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
233 </section>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
234 <!-- LongOrfs -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
235 <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
236 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
237 <has_n_lines n="398"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
238 <has_text_matching expression="CUFF\.20\.1.+"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
239 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
240 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
241 <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
242 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
243 <has_n_lines n="1330"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
244 <has_text_matching expression="CUFF\.20\.1.+"/>
5
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 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
247 <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
248 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
249 <has_n_lines n="398"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
250 <has_text_matching expression="CUFF\.20\.1.+"/>
5
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 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
253 <!-- Predict -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
254 <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
255 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
256 <has_n_lines n="62"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
257 <has_text_matching expression="CUFF\.9\.1.+"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
258 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
259 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
260 <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
261 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
262 <has_n_lines n="1312"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
263 <has_text_matching expression="CUFF\.9\.1.+"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
264 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
265 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
266 <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
267 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
268 <has_n_lines n="395"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
269 <has_text_matching expression="CUFF\.9\.1.+"/>
5
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 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
272 <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
273 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
274 <has_n_lines n="500"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
275 <has_text_matching expression="CUFF\.9\.1.+"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
276 </assert_contents>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
277 </output>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
278 <output name="out_plot">
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
279 <assert_contents>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
280 <has_size value="0"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
281 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
282 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
283 <!-- Others -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
284 <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
285 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
286 <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
287 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
288 </output>
0
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
289 </test>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
290 <!-- #3 -->
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
291 <test expect_num_outputs="9">
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
292 <param name="t" value="pasa_assemblies.fasta"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
293 <section name="lo">
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
294 <param name="gene_trans_map" value="pasa_genetransmap.txt"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
295 </section>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
296 <section name="oo">
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
297 <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,plot,log"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
298 </section>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
299 <!-- LongOrfs -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
300 <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
301 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
302 <has_n_lines n="534"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
303 <has_text_matching expression=">asmbl\_236\.p1.+"/>
5
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 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
306 <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
307 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
308 <has_n_lines n="1742"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
309 <has_text_matching expression="asmbl\_236.+"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
310 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
311 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
312 <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
313 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
314 <has_n_lines n="534"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
315 <has_text_matching expression=">asmbl\_236\.p1.+"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
316 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
317 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
318 <!-- Predict -->
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
319 <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
320 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
321 <has_n_lines n="204"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
322 <has_text_matching expression="asmbl\_99.+"/>
5
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 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
325 <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
326 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
327 <has_n_lines n="3560"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
328 <has_text_matching expression=">asmbl\_99\.p1.+"/>
5
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 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
331 <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
332 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
333 <has_n_lines n="1337"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
334 <has_text_matching expression="asmbl\_99.+"/>
5
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
335 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
336 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
337 <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
338 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
339 <has_n_lines n="1391"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
340 <has_text_matching expression=">asmbl\_99\.p1.+"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
341 </assert_contents>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
342 </output>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
343 <output name="out_plot">
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents: 5
diff changeset
344 <assert_contents>
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345 <has_size value="714868" delta="1000"/>
5
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346 </assert_contents>
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347 </output>
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348 <!-- Others -->
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349 <output name="out_log">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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350 <assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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351 <has_text_matching expression="transdecoder is finished.+"/>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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352 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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353 </output>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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354 </test>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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355 <!-- #4 -->
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356 <test expect_num_outputs="1">
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357 <param name="t" value="transcripts.fasta"/>
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358 <section name="po">
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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359 <conditional name="predict_cond">
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360 <param name="predict_sel" value="no"/>
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361 </conditional>
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362 </section>
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363 <!-- LongOrfs -->
6
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364 <output name="out_pep">
5
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365 <assert_contents>
6
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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366 <has_n_lines n="190"/>
d0d4cef4f967 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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367 <has_text_matching expression="CUFF\.9\.1.+"/>
5
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368 </assert_contents>
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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369 </output>
0
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370 </test>
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371 </tests>
5
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372 <help><![CDATA[
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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373 .. class:: infomark
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374
0
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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375 **What it does**
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376
5
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377 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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378
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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379 TransDecoder identifies likely coding sequences based on the following criteria:
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380
5
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381 - a minimum length open reading frame (ORF) is found in a transcript sequence.
0
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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382 - a log-likelihood score similar to what is computed by the GeneID software is > 0.
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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383 - 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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384 - 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).
5
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385 - a PSSM is built/trained/used to refine the start codon prediction.
0
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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386 - optional the putative peptide has a match to a Pfam domain above the noise cutoff score.
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387
5
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388 *Step 1*: Extract long open reading frames
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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389
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390 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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391
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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392 *Step 2*: (optional and not part of this wrapper)
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393
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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394 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>`_).
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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395
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396 *Step 3*: Predict the likely coding regions
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397
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398 Optionally apply results of homology searches in this step and re-run the whole analysis.
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399
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400 **Input**
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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401
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402 - FASTA file with transcripts
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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403 - (optional) gene-to-transcript identifier mapping file
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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404 - (optional) BLAST or Pfam database file (`details <https://github.com/TransDecoder/TransDecoder/wiki#including-homology-searches-as-orf-retention-criteria>`_)
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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405
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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406 **Output**
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407
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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408 *LongOrfs*
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409
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410 - longest ORFs (PEP/FASTA): all ORFs meeting the minimum length criteria, regardless of coding potential
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411 - longest ORFs (GFF3): positions of all ORFs as found in the target transcripts
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412 - longest ORFs (CDS/FASTA): the nucleotide coding sequence for all detected ORFs
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413
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414 *Predict*
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415
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416 - Results (PEP/FASTA): peptide sequences for the final candidate ORFs; all shorter candidates within longer ORFs were removed
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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417 - Results (CDS/FASTA): nucleotide sequences for coding regions of the final candidate ORFs
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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418 - Results (GFF3): positions within the target transcripts of the final selected ORFs
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419 - Results (BED): BED-formatted file describing ORF positions, best for viewing using GenomeView or IGV
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420 - Plots: sequence logos and scores (compressed PDF)
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421
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422 *Other*
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423
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424 - Log file
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425
c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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426 .. class:: infomark
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427
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428 **References**
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429
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430 More information are available on `GitHub <https://github.com/TransDecoder/TransDecoder>`_.
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431 ]]></help>
4
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432 <citations>
0
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433 <citation type="doi">10.1038/nprot.2013.084</citation>
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434 </citations>
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c6334cb383ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents: 4
diff changeset
435 </tool>