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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit a01a55b03c6160fa665e678131f9ac1318577ba0"
author iuc
date Sun, 21 Nov 2021 17:18:27 +0000
parents 4383070d29ed
children
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1 <tool id="trinotate" name="Trinotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>functional transcript annotation</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">3.2.2</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">trinotate</requirement>
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9 <requirement type="package" version="1.18">gnu-wget</requirement>
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10 </requirements>
4
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11 <xrefs>
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12 <xref type="bio.tools">trinotate</xref>
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13 </xrefs>
3
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14 <version_command><![CDATA[
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15 Trinotate version @TOOL_VERSION@
3
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16 ]]></version_command>
4
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17 <command detect_errors="exit_code"><![CDATA[
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19 #if str($cond_download.select_download) == "yes":
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20 Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate &&
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21 #else:
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22 ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite &&
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23 #end if
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25 Trinotate Trinotate.sqlite init --gene_trans_map '$gene_trans_map' --transcript_fasta $trinity --transdecoder_pep '$transdecoder' &&
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26 #if $blastp:
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27 Trinotate Trinotate.sqlite LOAD_swissprot_blastp '$blastp' &&
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28 #end if
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29 #if $blastx:
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30 Trinotate Trinotate.sqlite LOAD_swissprot_blastx '$blastx' &&
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31 #end if
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32 #if $hmmscan:
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33 Trinotate Trinotate.sqlite LOAD_pfam '$hmmscan' &&
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34 #end if
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35 #if $tmhmm:
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36 Trinotate Trinotate.sqlite LOAD_tmhmm '$tmhmm' &&
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37 #end if
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38 #if $signalp:
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39 Trinotate Trinotate.sqlite LOAD_signalp '$signalp' &&
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40 #end if
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41
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42 Trinotate Trinotate.sqlite report -E $report_option.E --pfam_cutoff $report_option.pfam_cutoff $report_option.incl_pep $report_option.incl_trans > '$trinotate_out'
0
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43
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44 ]]></command>
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45 <inputs>
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46 <param name="trinity" type="data" format="fasta" optional="false" label="Transcripts" help="Trinity output: Assembled Transcripts" />
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47 <param name="transdecoder" type="data" format="fasta" optional="false" label="Peptides" help="Transdecoder output: transdecoder_pep" />
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48 <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" />
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49 <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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50 <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)" />
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51 <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)" />
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52 <param name="tmhmm" type="data" format="tabular" optional="true" label="TMHMM on Peptides" help="[optional]"/>
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53 <param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" />
0
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54
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55 <conditional name="cond_download">
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56 <param name="select_download" type="select" label="Let Galaxy downloading the Trinotate Pre-generated Resource SQLite database">
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57 <option value="yes" selected="True">Yes</option>
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58 <option value="no">No, I will provide it</option>
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59 </param>
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60 <when value="no">
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61 <param name="trinotate_sqlite_in" type="data" format="sqlite" optional="false" label="Trinotate Pre-generated Resource SQLite database" help="https://data.broadinstitute.org/Trinity/__deprecated_trinotate_resources/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz" />
0
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62 </when>
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63 <when value="yes" />
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64 </conditional>
2
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65
0
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66 <section name="report_option" title="Report options" expanded="False">
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67 <param argument="-E" type="float" value="1e-5" label="Maximum E-value for reporting best blast hit and associated annotations." />
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68 <param argument="--pfam_cutoff" type="select" label="PFAM cutoff">
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69 <option value="DNC">DNC : domain noise cutoff</option>
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70 <option value="DGC">DGC : domain gathering cutoff</option>
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71 <option value="DTC">DTC : domain trusted cutoff</option>
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72 <option value="SNC">SNC : sequence noise cutoff</option>
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73 <option value="SGC">SGC : sequence gathering cutoff</option>
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74 <option value="STC">STC : sequence trusted cutoff</option>
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75 </param>
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76 <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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77 <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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78 </section>
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79 <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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80 </inputs>
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81 <outputs>
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82 <data name="trinotate_out" format="tabular" label="Trinotate output" >
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83 <actions>
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84 <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" />
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85 </actions>
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86 </data>
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87 <data name="trinotate_sqlite" format="sqlite" from_work_dir="Trinotate.sqlite" label="Trinotate sqlite database" >
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88 <filter>keep_sqlite</filter>
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89 </data>
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="trinity" ftype="fasta" value="Trinity.fasta" />
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94 <param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" />
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95 <param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" />
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96 <param name="blastp" ftype="tabular" value="swissprot.blastp.outfmt6" />
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97 <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" />
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98 <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" />
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99 <param name="tmhmm" ftype="tabular" value="tmhmm.out" />
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100 <param name="signalp" ftype="tabular" value="signalp.out" />
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101 <output name="trinotate_out" file="trinotate_annotation_report.xls" />
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102 </test>
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103 <test>
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104 <param name="trinity" ftype="fasta" value="Trinity.fasta" />
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105 <param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" />
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106 <param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" />
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107 <param name="blastp" ftype="tabular" value="swissprot.blastp.outfmt6" />
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108 <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" />
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109 <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" />
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110 <section name="report_option">
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111 <param name="incl_pep" value="true" />
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112 <param name="incl_trans" value="true" />
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113 </section>
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114 <param name="keep_sqlite" value="true" />
4
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115 <output name="trinotate_out" ftype="tabular" >
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116 <assert_contents>
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117 <has_size value="573911" delta="100"/>
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118 <has_text text="Meiotically up-regulated gene 56 protein"/>
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119 <has_text text="Serine/threonine-protein kinase tor1"/>
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120 </assert_contents>
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121 </output>
0
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122 </test>
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123 </tests>
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124 <help><![CDATA[
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125 .. class:: infomark
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126
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127 **What it does**
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128
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129 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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130
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131 .. _Trinotate: https://trinotate.github.io/
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132
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133 --------
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134
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135 **Suggested upstream Galaxy tools**
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136
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137 Transcripts
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138
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139 - Trinity: iuc/trinity_
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140
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141 .. _trinity: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a
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142
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143 Peptides
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144
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145 - TransDecoder: iuc/transdecoder_
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146
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147 .. _transdecoder: https://toolshed.g2.bx.psu.edu/repository?repository_id=7a2a8151a50f8099
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148
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149 Genes to transcripts map
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150
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151 - Generate gene to transcript map for Trinity assembly: iuc/trinity_gene_to_trans_map_
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152
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153 .. _trinity_gene_to_trans_map: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a
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154
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155 BLASTP: Peptides vs Uniprot.SwissProt
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156
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157 - NCBI BLAST+ blastp: devteam/ncbi_blast_plus_
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158
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159 .. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c
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160
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161 BLASTX: Transcripts vs Uniprot.SwissProt
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162
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163 - NCBI BLAST+ blastx: devteam/ncbi_blast_plus_
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164
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165 .. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c
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166
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167 HMMER hmmscan: Peptides vs PFAM
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168
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169 - HMMER hmmscan: iuc/hmmer_hmmscan_
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170
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171 .. _hmmer_hmmscan: https://toolshed.g2.bx.psu.edu/repository?repository_id=a2cc4683090b1800
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172
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173 TMHMM on Peptides
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174
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175 - TMHMM 2.0: peterjc/tmhmm_and_signalp_
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176
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177 .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a
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178
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179 SignalP on Peptides
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180
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181 - SignalP 3.0: peterjc/tmhmm_and_signalp_
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182
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183 .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a
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184
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185 --------
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186
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187 **Output**
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188
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189 The output has the following column headers:
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190
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191
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192 ====== =======================
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193 Column Description
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194 ------ -----------------------
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195 0 #gene_id
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196 1 transcript_id
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197 2 sprot_Top_BLASTX_hit
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198 3 RNAMMER
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199 4 prot_id
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200 5 prot_coords
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201 6 sprot_Top_BLASTP_hit
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202 7 custom_pombe_pep_BLASTX
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203 8 custom_pombe_pep_BLASTP
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204 9 Pfam
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205 10 SignalP
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206 11 TmHMM
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207 12 eggnog
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208 13 Kegg
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209 14 gene_ontology_blast
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210 15 gene_ontology_pfam
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211 16 transcript
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212 17 peptide
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213 ====== =======================
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214
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215 ]]></help>
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216 <citations>
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217 <citation type="doi">10.1038/nbt.1883</citation>
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218 </citations>
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219 </tool>