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Updating tools/trinotate from version 3.2.2 to 4.0.2 #5270

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Updating tools/trinotate from version 3.2.2 to 4.0.2 #5270

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b364ff3
Updating tools/trinotate from version 3.2.2 to 4.0.0
Apr 20, 2023
2e7ab2b
Updating tools/trinotate from version 4.0.0 to 4.0.1
Jun 5, 2023
a10aeaa
Updating tools/trinotate from version 4.0.1 to 4.0.2
Nov 6, 2023
5c46857
fix linting
bgruening May 19, 2024
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84 changes: 41 additions & 43 deletions tools/trinotate/trinotate.xml
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Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
<tool id="trinotate" name="Trinotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
<description>functional transcript annotation</description>
<macros>
<token name="@TOOL_VERSION@">3.2.2</token>
<token name="@TOOL_VERSION@">4.0.2</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<xrefs>
<xref type="bio.tools">trinotate</xref>
</xrefs>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">trinotate</requirement>
<requirement type="package" version="1.18">gnu-wget</requirement>
</requirements>
<xrefs>
<xref type="bio.tools">trinotate</xref>
</xrefs>
<version_command><![CDATA[
Trinotate version @TOOL_VERSION@
]]></version_command>
Expand Down Expand Up @@ -43,28 +43,26 @@ Trinotate Trinotate.sqlite report -E $report_option.E --pfam_cutoff $report_opti

]]></command>
<inputs>
<param name="trinity" type="data" format="fasta" optional="false" label="Transcripts" help="Trinity output: Assembled Transcripts" />
<param name="transdecoder" type="data" format="fasta" optional="false" label="Peptides" help="Transdecoder output: transdecoder_pep" />
<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" />
<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)" />
<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)" />
<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)" />
<param name="trinity" type="data" format="fasta" optional="false" label="Transcripts" help="Trinity output: Assembled Transcripts"/>
<param name="transdecoder" type="data" format="fasta" optional="false" label="Peptides" help="Transdecoder output: transdecoder_pep"/>
<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"/>
<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)"/>
<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)"/>
<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)"/>
<param name="tmhmm" type="data" format="tabular" optional="true" label="TMHMM on Peptides" help="[optional]"/>
<param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" />

<param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]"/>
<conditional name="cond_download">
<param name="select_download" type="select" label="Let Galaxy downloading the Trinotate Pre-generated Resource SQLite database">
<option value="yes" selected="True">Yes</option>
<option value="no">No, I will provide it</option>
</param>
<when value="no">
<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" />
<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"/>
</when>
<when value="yes" />
<when value="yes"/>
</conditional>

<section name="report_option" title="Report options" expanded="False">
<param argument="-E" type="float" value="1e-5" label="Maximum E-value for reporting best blast hit and associated annotations." />
<param argument="-E" type="float" value="1e-5" label="Maximum E-value for reporting best blast hit and associated annotations."/>
<param argument="--pfam_cutoff" type="select" label="PFAM cutoff">
<option value="DNC">DNC : domain noise cutoff</option>
<option value="DGC">DGC : domain gathering cutoff</option>
Expand All @@ -73,46 +71,46 @@ Trinotate Trinotate.sqlite report -E $report_option.E --pfam_cutoff $report_opti
<option value="SGC">SGC : sequence gathering cutoff</option>
<option value="STC">STC : sequence trusted cutoff</option>
</param>
<param argument="--incl_pep" type="boolean" truevalue="--incl_pep" falsevalue="" checked="false" label="Add the protein sequence data in the tab delimited report" />
<param argument="--incl_trans" type="boolean" truevalue="--incl_trans" falsevalue="" checked="false" label="Add the transcript sequence data in the tab delimited report" />
<param argument="--incl_pep" type="boolean" truevalue="--incl_pep" falsevalue="" checked="false" label="Add the protein sequence data in the tab delimited report"/>
<param argument="--incl_trans" type="boolean" truevalue="--incl_trans" falsevalue="" checked="false" label="Add the transcript sequence data in the tab delimited report"/>
</section>
<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" />
<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"/>
</inputs>
<outputs>
<data name="trinotate_out" format="tabular" label="Trinotate output" >
<data name="trinotate_out" format="tabular" label="Trinotate output">
<actions>
<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" />
<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"/>
</actions>
</data>
<data name="trinotate_sqlite" format="sqlite" from_work_dir="Trinotate.sqlite" label="Trinotate sqlite database" >
<data name="trinotate_sqlite" format="sqlite" from_work_dir="Trinotate.sqlite" label="Trinotate sqlite database">
<filter>keep_sqlite</filter>
</data>
</outputs>
<tests>
<test>
<param name="trinity" ftype="fasta" value="Trinity.fasta" />
<param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" />
<param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" />
<param name="blastp" ftype="tabular" value="swissprot.blastp.outfmt6" />
<param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" />
<param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" />
<param name="tmhmm" ftype="tabular" value="tmhmm.out" />
<param name="signalp" ftype="tabular" value="signalp.out" />
<output name="trinotate_out" file="trinotate_annotation_report.xls" />
<test expect_num_outputs="1">
<param name="trinity" value="Trinity.fasta" ftype="fasta"/>
<param name="transdecoder" value="Trinity.fasta.transdecoder.pep" ftype="fasta"/>
<param name="gene_trans_map" value="Trinity.fasta.gene_to_trans_map" ftype="tabular"/>
<param name="blastp" value="swissprot.blastp.outfmt6" ftype="tabular"/>
<param name="blastx" value="swissprot.blastx.outfmt6" ftype="tabular"/>
<param name="hmmscan" value="TrinotatePFAM.out" ftype="txt"/>
<param name="tmhmm" value="tmhmm.out" ftype="tabular"/>
<param name="signalp" value="signalp.out" ftype="tabular"/>
<output name="trinotate_out" file="trinotate_annotation_report.xls"/>
</test>
<test>
<param name="trinity" ftype="fasta" value="Trinity.fasta" />
<param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" />
<param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" />
<param name="blastp" ftype="tabular" value="swissprot.blastp.outfmt6" />
<param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" />
<param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" />
<test expect_num_outputs="2">
<param name="trinity" value="Trinity.fasta" ftype="fasta"/>
<param name="transdecoder" value="Trinity.fasta.transdecoder.pep" ftype="fasta"/>
<param name="gene_trans_map" value="Trinity.fasta.gene_to_trans_map" ftype="tabular"/>
<param name="blastp" value="swissprot.blastp.outfmt6" ftype="tabular"/>
<param name="blastx" value="swissprot.blastx.outfmt6" ftype="tabular"/>
<param name="hmmscan" value="TrinotatePFAM.out" ftype="txt"/>
<section name="report_option">
<param name="incl_pep" value="true" />
<param name="incl_trans" value="true" />
<param name="incl_pep" value="true"/>
<param name="incl_trans" value="true"/>
</section>
<param name="keep_sqlite" value="true" />
<output name="trinotate_out" ftype="tabular" >
<param name="keep_sqlite" value="true"/>
<output name="trinotate_out" ftype="tabular">
<assert_contents>
<has_size value="573911" delta="100"/>
<has_text text="Meiotically up-regulated gene 56 protein"/>
Expand Down
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