From b364ff3f289cbd9b36f85d88b63ff4b1d390a3d1 Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Thu, 20 Apr 2023 12:50:49 +0000
Subject: [PATCH 1/4] Updating tools/trinotate from version 3.2.2 to 4.0.0

---
 tools/trinotate/trinotate.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/trinotate/trinotate.xml b/tools/trinotate/trinotate.xml
index 3810f6bcfce..60c97101b71 100644
--- a/tools/trinotate/trinotate.xml
+++ b/tools/trinotate/trinotate.xml
@@ -1,7 +1,7 @@
 <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@">4.0.0</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>

From 2e7ab2b0c11d1125df464bed5c5d24c2164d5f70 Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Mon, 5 Jun 2023 04:46:12 +0000
Subject: [PATCH 2/4] Updating tools/trinotate from version 4.0.0 to 4.0.1

---
 tools/trinotate/trinotate.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/trinotate/trinotate.xml b/tools/trinotate/trinotate.xml
index 60c97101b71..0d53242696d 100644
--- a/tools/trinotate/trinotate.xml
+++ b/tools/trinotate/trinotate.xml
@@ -1,7 +1,7 @@
 <tool id="trinotate" name="Trinotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>functional transcript annotation</description>
     <macros>
-        <token name="@TOOL_VERSION@">4.0.0</token>
+        <token name="@TOOL_VERSION@">4.0.1</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>

From a10aeaaa36b0d2506e230bbf6d310c843c3693c8 Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Mon, 6 Nov 2023 19:41:48 +0000
Subject: [PATCH 3/4] Updating tools/trinotate from version 4.0.1 to 4.0.2

---
 tools/trinotate/trinotate.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/trinotate/trinotate.xml b/tools/trinotate/trinotate.xml
index 0d53242696d..e4ea02d3ec9 100644
--- a/tools/trinotate/trinotate.xml
+++ b/tools/trinotate/trinotate.xml
@@ -1,7 +1,7 @@
 <tool id="trinotate" name="Trinotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>functional transcript annotation</description>
     <macros>
-        <token name="@TOOL_VERSION@">4.0.1</token>
+        <token name="@TOOL_VERSION@">4.0.2</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>

From 5c46857da00b6062e148fd6dd79c072ee23904a4 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sun, 19 May 2024 10:24:42 +0200
Subject: [PATCH 4/4] fix linting

---
 tools/trinotate/trinotate.xml | 82 +++++++++++++++++------------------
 1 file changed, 40 insertions(+), 42 deletions(-)

diff --git a/tools/trinotate/trinotate.xml b/tools/trinotate/trinotate.xml
index e4ea02d3ec9..0961801db48 100644
--- a/tools/trinotate/trinotate.xml
+++ b/tools/trinotate/trinotate.xml
@@ -4,13 +4,13 @@
         <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>
@@ -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>
@@ -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"/>