Mercurial > repos > iuc > trinotate
annotate trinotate.xml @ 3:4383070d29ed draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 7d7285e1c16a9058178a51c804409319e6685454"
author | iuc |
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date | Fri, 14 Aug 2020 16:54:16 -0400 |
parents | 6fd16fad465d |
children | 2b093007fab9 |
rev | line source |
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3
4383070d29ed
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 7d7285e1c16a9058178a51c804409319e6685454"
iuc
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1 <tool id="trinotate" name="Trinotate" version="3.2.1"> |
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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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2 <requirements> |
3
4383070d29ed
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 7d7285e1c16a9058178a51c804409319e6685454"
iuc
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3 <requirement type="package" version="3.2.1">trinotate</requirement> |
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499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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4 <requirement type="package" version="1.18">gnu-wget</requirement> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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5 </requirements> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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6 <stdio> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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7 <exit_code range="1:" /> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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8 </stdio> |
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4383070d29ed
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 7d7285e1c16a9058178a51c804409319e6685454"
iuc
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9 <version_command><![CDATA[ |
4383070d29ed
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 7d7285e1c16a9058178a51c804409319e6685454"
iuc
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10 Trinotate version 3.2.1 |
4383070d29ed
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 7d7285e1c16a9058178a51c804409319e6685454"
iuc
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11 ]]></version_command> |
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499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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12 <command><![CDATA[ |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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13 |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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14 #if str($cond_download.select_download) == "yes": |
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6fd16fad465d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 4aa8226ad3031636041eaa6f29a7fb4721dcdc43
iuc
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15 Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate && |
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499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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16 #else: |
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6fd16fad465d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 4aa8226ad3031636041eaa6f29a7fb4721dcdc43
iuc
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17 ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite && |
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499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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18 #end if |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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19 |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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20 Trinotate Trinotate.sqlite init --gene_trans_map '$gene_trans_map' --transcript_fasta $trinity --transdecoder_pep '$transdecoder' && |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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21 #if $blastp: |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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22 Trinotate Trinotate.sqlite LOAD_swissprot_blastp '$blastp' && |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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23 #end if |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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24 #if $blastx: |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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changeset
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25 Trinotate Trinotate.sqlite LOAD_swissprot_blastx '$blastx' && |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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26 #end if |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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27 #if $hmmscan: |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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28 Trinotate Trinotate.sqlite LOAD_pfam '$hmmscan' && |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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29 #end if |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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30 #if $tmhmm: |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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31 Trinotate Trinotate.sqlite LOAD_tmhmm '$tmhmm' && |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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32 #end if |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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33 #if $signalp: |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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34 Trinotate Trinotate.sqlite LOAD_signalp '$signalp' && |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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35 #end if |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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36 |
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6fd16fad465d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 4aa8226ad3031636041eaa6f29a7fb4721dcdc43
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37 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
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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38 |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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39 ]]></command> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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40 <inputs> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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41 <param name="trinity" type="data" format="fasta" optional="false" label="Transcripts" help="Trinity output: Assembled Transcripts" /> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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42 <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
iuc
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43 <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
iuc
parents:
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44 <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)" /> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
parents:
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45 <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
iuc
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46 <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
iuc
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47 <param name="tmhmm" type="data" format="tabular" optional="true" label="TMHMM on Peptides" help="[optional]"/> |
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6fd16fad465d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 4aa8226ad3031636041eaa6f29a7fb4721dcdc43
iuc
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48 <param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" /> |
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499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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49 |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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50 <conditional name="cond_download"> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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51 <param name="select_download" type="select" label="Let Galaxy downloading the Trinotate Pre-generated Resource SQLite database"> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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52 <option value="yes" selected="True">Yes</option> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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53 <option value="no">No, I will provide it</option> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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54 </param> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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55 <when value="no"> |
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9e61bc67866f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 910addf8de57fa9fa678c8a69c558390f5a16601
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56 <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" /> |
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499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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57 </when> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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58 <when value="yes" /> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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59 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 4aa8226ad3031636041eaa6f29a7fb4721dcdc43
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60 |
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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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61 <section name="report_option" title="Report options" expanded="False"> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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62 <param argument="-E" type="float" value="1e-5" label="Maximum E-value for reporting best blast hit and associated annotations." /> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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63 <param argument="--pfam_cutoff" type="select" label="PFAM cutoff"> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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64 <option value="DNC">DNC : domain noise cutoff</option> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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65 <option value="DGC">DGC : domain gathering cutoff</option> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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66 <option value="DTC">DTC : domain trusted cutoff</option> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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67 <option value="SNC">SNC : sequence noise cutoff</option> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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68 <option value="SGC">SGC : sequence gathering cutoff</option> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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69 <option value="STC">STC : sequence trusted cutoff</option> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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70 </param> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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71 <param argument="--incl_pep" type="boolean" truevalue="--incl_pep" falsevalue="" checked="false" label="Add the protein sequence data in the tab delimited report" /> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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72 <param argument="--incl_trans" type="boolean" truevalue="--incl_trans" falsevalue="" checked="false" label="Add the transcript sequence data in the tab delimited report" /> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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73 </section> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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74 <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" /> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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75 </inputs> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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76 <outputs> |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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77 <data name="trinotate_out" format="tabular" label="Trinotate output" > |
499d87c45612
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
iuc
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78 <actions> |
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79 <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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80 </actions> |
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81 </data> |
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82 <data name="trinotate_sqlite" format="sqlite" from_work_dir="Trinotate.sqlite" label="Trinotate sqlite database" > |
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83 <filter>keep_sqlite</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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84 </data> |
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85 </outputs> |
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86 <tests> |
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87 <test> |
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88 <param name="trinity" ftype="fasta" value="Trinity.fasta" /> |
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89 <param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" /> |
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90 <param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" /> |
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91 <param name="blastp" ftype="tabular" value="swissprot.blastp.outfmt6" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
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92 <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" /> |
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93 <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" /> |
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94 <param name="tmhmm" ftype="tabular" value="tmhmm.out" /> |
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95 <param name="signalp" ftype="tabular" value="signalp.out" /> |
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96 <output name="trinotate_out" file="trinotate_annotation_report.xls" /> |
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97 </test> |
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98 <test> |
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99 <param name="trinity" ftype="fasta" value="Trinity.fasta" /> |
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100 <param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" /> |
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101 <param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" /> |
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102 <param name="blastp" ftype="tabular" value="swissprot.blastp.outfmt6" /> |
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103 <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" /> |
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104 <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" /> |
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105 <section name="report_option"> |
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106 <param name="incl_pep" value="true" /> |
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107 <param name="incl_trans" value="true" /> |
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108 </section> |
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109 <param name="keep_sqlite" value="true" /> |
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110 <output name="trinotate_out" file="trinotate_annotation_report_minus_tmhmm_signalp.xls" /> |
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111 </test> |
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112 </tests> |
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113 <help><![CDATA[ |
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114 .. class:: infomark |
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115 |
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116 **What it does** |
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117 |
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118 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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119 |
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120 .. _Trinotate: https://trinotate.github.io/ |
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121 |
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122 -------- |
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123 |
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124 **Suggested upstream Galaxy tools** |
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125 |
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126 Transcripts |
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127 |
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128 - Trinity: iuc/trinity_ |
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129 |
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130 .. _trinity: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a |
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131 |
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132 Peptides |
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133 |
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134 - TransDecoder: iuc/transdecoder_ |
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135 |
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136 .. _transdecoder: https://toolshed.g2.bx.psu.edu/repository?repository_id=7a2a8151a50f8099 |
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137 |
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138 Genes to transcripts map |
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139 |
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140 - Generate gene to transcript map for Trinity assembly: iuc/trinity_gene_to_trans_map_ |
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141 |
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142 .. _trinity_gene_to_trans_map: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a |
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143 |
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144 BLASTP: Peptides vs Uniprot.SwissProt |
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145 |
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146 - NCBI BLAST+ blastp: devteam/ncbi_blast_plus_ |
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147 |
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148 .. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c |
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149 |
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150 BLASTX: Transcripts vs Uniprot.SwissProt |
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151 |
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152 - NCBI BLAST+ blastx: devteam/ncbi_blast_plus_ |
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153 |
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154 .. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c |
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155 |
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156 HMMER hmmscan: Peptides vs PFAM |
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157 |
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158 - HMMER hmmscan: iuc/hmmer_hmmscan_ |
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159 |
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160 .. _hmmer_hmmscan: https://toolshed.g2.bx.psu.edu/repository?repository_id=a2cc4683090b1800 |
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161 |
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162 TMHMM on Peptides |
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163 |
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164 - TMHMM 2.0: peterjc/tmhmm_and_signalp_ |
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165 |
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166 .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a |
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167 |
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168 SignalP on Peptides |
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169 |
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170 - SignalP 3.0: peterjc/tmhmm_and_signalp_ |
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171 |
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172 .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a |
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173 |
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174 -------- |
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175 |
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176 **Output** |
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177 |
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178 The output has the following column headers: |
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179 |
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180 |
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181 ====== ======================= |
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182 Column Description |
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183 ------ ----------------------- |
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184 0 #gene_id |
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185 1 transcript_id |
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186 2 sprot_Top_BLASTX_hit |
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187 3 RNAMMER |
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188 4 prot_id |
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189 5 prot_coords |
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190 6 sprot_Top_BLASTP_hit |
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191 7 custom_pombe_pep_BLASTX |
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192 8 custom_pombe_pep_BLASTP |
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193 9 Pfam |
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194 10 SignalP |
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195 11 TmHMM |
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196 12 eggnog |
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197 13 Kegg |
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198 14 gene_ontology_blast |
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199 15 gene_ontology_pfam |
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200 16 transcript |
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201 17 peptide |
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202 ====== ======================= |
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203 |
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204 ]]></help> |
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205 <citations> |
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206 <citation type="doi">10.1038/nbt.1883</citation> |
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207 </citations> |
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208 </tool> |