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annotate trinotate.xml @ 0:499d87c45612 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
author iuc
date Tue, 15 Nov 2016 09:17:29 -0500
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499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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1 <tool id="trinotate" name="Trinotate" version="3.0.1.0">
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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2 <requirements>
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3 <requirement type="package" version="3.0.1">trinotate</requirement>
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4 <requirement type="package" version="1.18">gnu-wget</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <version_command>
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10 <![CDATA[
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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11 Trinotate version 3.0.1
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12 ]]>
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13 </version_command>
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14 <command><![CDATA[
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15
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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16 #if str($cond_download.select_download) == "yes":
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17 wget --no-verbose 'https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz' -O Trinotate.sqlite.gz &&
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18 gunzip Trinotate.sqlite.gz &&
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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19 #else:
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20 ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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21 #end if
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22
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23 Trinotate Trinotate.sqlite init --gene_trans_map '$gene_trans_map' --transcript_fasta $trinity --transdecoder_pep '$transdecoder' &&
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24 #if $blastp:
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25 Trinotate Trinotate.sqlite LOAD_swissprot_blastp '$blastp' &&
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26 #end if
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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27 #if $blastx:
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28 Trinotate Trinotate.sqlite LOAD_swissprot_blastx '$blastx' &&
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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29 #end if
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30 #if $hmmscan:
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31 Trinotate Trinotate.sqlite LOAD_pfam '$hmmscan' &&
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32 #end if
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33 #if $tmhmm:
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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34 Trinotate Trinotate.sqlite LOAD_tmhmm '$tmhmm' &&
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35 #end if
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36 #if $signalp:
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37 Trinotate Trinotate.sqlite LOAD_signalp '$signalp' &&
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38 #end if
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39
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40 Trinotate Trinotate.sqlite report -E $report_option.E --pfam_cutoff $report_option.pfam_cutoff $report_option.incl_pep $report_option.incl_trans > '$trinotate_out';
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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41
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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42 ]]></command>
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43 <inputs>
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44 <param name="trinity" type="data" format="fasta" optional="false" label="Transcripts" help="Trinity output: Assembled Transcripts" />
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45 <param name="transdecoder" type="data" format="fasta" optional="false" label="Peptides" help="Transdecoder output: transdecoder_pep" />
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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46 <param name="gene_trans_map" type="data" format="tabular" optional="false" label="Genes to transcripts map" help="Genes to transcripts map output. Containing correspondance between gene ids and transcript ids based on the name of transcripts assembled by Trinity" />
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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47 <param name="blastp" type="data" format="tabular" optional="true" label="BLASTP: Peptides vs Uniprot.SwissProt" help="[optional] NCBI BLAST+ blastp output. Output format: Tabular (standard 12 columns)" />
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48 <param name="blastx" type="data" format="tabular" optional="true" label="BLASTX: Transcripts vs Uniprot.SwissProt" help="[optional] NCBI BLAST+ blastx output. Output format: Tabular (standard 12 columns)" />
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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49 <param name="hmmscan" type="data" format="txt" optional="true" label="HMMER hmmscan: Peptides vs PFAM" help="[optional] HMMER hmmscan output: Table of per-domain hits. Output format: Table of per-domain hits (--domtblout)" />
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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50 <param name="tmhmm" type="data" format="tabular" optional="true" label="TMHMM on Peptides" help="[optional]"/>
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51 <param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" />
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52
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53 <conditional name="cond_download">
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54 <param name="select_download" type="select" label="Let Galaxy downloading the Trinotate Pre-generated Resource SQLite database">
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55 <option value="yes" selected="True">Yes</option>
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56 <option value="no">No, I will provide it</option>
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57 </param>
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58 <when value="no">
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59 <param name="trinotate_sqlite_in" type="data" format="sqlite" optional="false" label="Trinotate Pre-generated Resource SQLite database" help="https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz" />
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60 </when>
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61 <when value="yes" />
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62 </conditional>
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63
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64 <section name="report_option" title="Report options" expanded="False">
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65 <param argument="-E" type="float" value="1e-5" label="Maximum E-value for reporting best blast hit and associated annotations." />
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66 <param argument="--pfam_cutoff" type="select" label="PFAM cutoff">
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67 <option value="DNC">DNC : domain noise cutoff</option>
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68 <option value="DGC">DGC : domain gathering cutoff</option>
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69 <option value="DTC">DTC : domain trusted cutoff</option>
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70 <option value="SNC">SNC : sequence noise cutoff</option>
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71 <option value="SGC">SGC : sequence gathering cutoff</option>
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72 <option value="STC">STC : sequence trusted cutoff</option>
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73 </param>
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74 <param argument="--incl_pep" type="boolean" truevalue="--incl_pep" falsevalue="" checked="false" label="Add the protein sequence data in the tab delimited report" />
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75 <param argument="--incl_trans" type="boolean" truevalue="--incl_trans" falsevalue="" checked="false" label="Add the transcript sequence data in the tab delimited report" />
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76 </section>
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77 <param name="keep_sqlite" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep the sqlite database file: Trinotate.sqlite" help="Can be used for visualization purpose" />
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78 </inputs>
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79 <outputs>
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80 <data name="trinotate_out" format="tabular" label="Trinotate output" >
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81 <actions>
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82 <action name="column_names" type="metadata" default="gene_id,transcript_id,sprot_Top_BLASTX_hit,RNAMMER,prot_id,prot_coords,sprot_Top_BLASTP_hit,custom_pombe_pep_BLASTX,custom_pombe_pep_BLASTP,Pfam,SignalP,TmHMM,eggnog,Kegg,gene_ontology_blast,gene_ontology_pfam,transcript,peptide" />
499d87c45612 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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83 </actions>
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84 </data>
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85 <data name="trinotate_sqlite" format="sqlite" from_work_dir="Trinotate.sqlite" label="Trinotate sqlite database" >
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86 <filter>keep_sqlite</filter>
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87 </data>
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88 </outputs>
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89 <tests>
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90 <test>
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91 <param name="trinity" ftype="fasta" value="Trinity.fasta" />
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92 <param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" />
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93 <param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" />
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94 <param name="blastp" ftype="tabular" value="swissprot.blastp.outfmt6" />
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95 <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" />
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96 <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" />
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97 <param name="tmhmm" ftype="tabular" value="tmhmm.out" />
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98 <param name="signalp" ftype="tabular" value="signalp.out" />
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99 <output name="trinotate_out" file="trinotate_annotation_report.xls" />
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100 </test>
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101 <test>
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102 <param name="trinity" ftype="fasta" value="Trinity.fasta" />
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103 <param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" />
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104 <param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" />
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105 <param name="blastp" ftype="tabular" value="swissprot.blastp.outfmt6" />
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106 <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" />
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107 <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" />
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108 <section name="report_option">
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109 <param name="incl_pep" value="true" />
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110 <param name="incl_trans" value="true" />
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111 </section>
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112 <param name="keep_sqlite" value="true" />
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113 <output name="trinotate_out" file="trinotate_annotation_report_minus_tmhmm_signalp.xls" />
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114 </test>
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115 </tests>
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116 <help><![CDATA[
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117 .. class:: infomark
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118
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119 **What it does**
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120
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121 Trinotate_ is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.
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122
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123 .. _Trinotate: https://trinotate.github.io/
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124
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125 --------
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126
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127 **Suggested upstream Galaxy tools**
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128
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129 Transcripts
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130
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131 - Trinity: iuc/trinity_
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132
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133 .. _trinity: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a
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134
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135 Peptides
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136
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137 - TransDecoder: iuc/transdecoder_
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138
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139 .. _transdecoder: https://toolshed.g2.bx.psu.edu/repository?repository_id=7a2a8151a50f8099
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140
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141 Genes to transcripts map
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142
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143 - Generate gene to transcript map for Trinity assembly: iuc/trinity_gene_to_trans_map_
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144
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145 .. _trinity_gene_to_trans_map: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a
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146
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147 BLASTP: Peptides vs Uniprot.SwissProt
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148
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149 - NCBI BLAST+ blastp: devteam/ncbi_blast_plus_
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150
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151 .. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c
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152
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153 BLASTX: Transcripts vs Uniprot.SwissProt
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154
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155 - NCBI BLAST+ blastx: devteam/ncbi_blast_plus_
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156
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157 .. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c
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158
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159 HMMER hmmscan: Peptides vs PFAM
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160
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161 - HMMER hmmscan: iuc/hmmer_hmmscan_
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162
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163 .. _hmmer_hmmscan: https://toolshed.g2.bx.psu.edu/repository?repository_id=a2cc4683090b1800
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164
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165 TMHMM on Peptides
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166
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167 - TMHMM 2.0: peterjc/tmhmm_and_signalp_
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168
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169 .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a
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170
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171 SignalP on Peptides
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172
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173 - SignalP 3.0: peterjc/tmhmm_and_signalp_
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174
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175 .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a
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176
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177
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178 Trinotate Pre-generated Resource SQLite database
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179
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180 - You can provide the SQLite database yourself, if Galaxy have trouble to download it : https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz
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181
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182 --------
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183
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184 **Output**
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185
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186 The output has the following column headers:
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187
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188
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189 ====== =======================
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190 Column Description
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191 ------ -----------------------
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192 0 #gene_id
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193 1 transcript_id
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194 2 sprot_Top_BLASTX_hit
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195 3 RNAMMER
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196 4 prot_id
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197 5 prot_coords
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198 6 sprot_Top_BLASTP_hit
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199 7 custom_pombe_pep_BLASTX
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200 8 custom_pombe_pep_BLASTP
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201 9 Pfam
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202 10 SignalP
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203 11 TmHMM
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204 12 eggnog
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205 13 Kegg
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206 14 gene_ontology_blast
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207 15 gene_ontology_pfam
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208 16 transcript
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209 17 peptide
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210 ====== =======================
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211
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212 ]]></help>
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213 <citations>
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214 <citation type="doi">10.1038/nbt.1883</citation>
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215 </citations>
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216 </tool>