From 235ea8ab19f510a033ca0c5aff624482396a15ce Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 26 Sep 2023 17:41:51 +0200
Subject: [PATCH 1/8] expression (1/?)

---
 tools/genenotebook/genenotebook_build.xml | 46 ++++++++++++++++-------
 tools/genenotebook/macros.xml             |  2 +-
 tools/genenotebook/test-data/exp.tsv      |  4 +-
 3 files changed, 35 insertions(+), 17 deletions(-)

diff --git a/tools/genenotebook/genenotebook_build.xml b/tools/genenotebook/genenotebook_build.xml
index aa054fb..bbbc836 100644
--- a/tools/genenotebook/genenotebook_build.xml
+++ b/tools/genenotebook/genenotebook_build.xml
@@ -57,11 +57,16 @@
         #end if
 
         #for exp in $annot.expression:
-            genoboo add transcriptome @CONNECT_INFO@
-                --sample-name '${exp.sample_name}'
-                --replica-group '${exp.replica_group}'
-                --sample-description '${exp.sample_description}'
-                '${exp.counts}';
+                genoboo add expression @CONNECT_INFO@
+                    #for replica in $exp.replicas:
+                        --replicas '${replica.replicas}'
+                    #end for
+                    #for replica_group_name in $exp.expression_replicas_names:
+                        --sample-description '${replica_group_name.replica_names}'
+                    #end for
+                    --sample-description '${exp.sample_description}'
+                    '${exp.public}'
+                    '${exp.counts}';
         #end for
     #end for
 #end for
@@ -121,9 +126,14 @@
 
                 <repeat name="expression" title="Expression data">
                     <param name="counts" label="Expression data" optional="true" type="data" format="tsv" />
-                    <param argument="--sample-name" name="sample_name" label="Unique sample name" type="text" />
-                    <param argument="--replica-group" name="replica_group" label="Identifier to group samples that belong to the same experiment" type="text" />
-                    <param argument="--sample-description" name="sample_description" label="Description of the experiment" type="text" />
+                    <repeat name="expression_replicas" title="Expression replicas">
+                        <param argument="--replicas" name="replicas" label="Comma-separated replica column positions" type="text" help="Comma-separated column positions, which are part of the same replica group. Can be set multiple times for multiple groups. The replica group name will be the first column, unless replica-names is set" />
+                    </repeat>
+                    <repeat name="expression_replicas_names" title="Expression replicas">
+                        <param argument="--replica-names" name="replica_names" label="Identifier to group samples that belong to the same experiment" type="text"  help="Name of the replica group. Will defaut to the first column header if not set. Can be set multiple time (for each replica group). Will match replica groups in order, whether they are multiple of single columns."/>
+                    </repeat>
+                    <param argument="--sample-description" name="sample_description" label="Description of the experiment" type="text" help="Name of the replica group. Will defaut to the first column header if not set. Can be set multiple time (for each replica group). Will match replica groups in order, whether they are multiple or single columns." />
+                    <param name="public" label="Public access" type="boolean" truevalue="--public" falsevalue="" value="false" />
                 </repeat>
             </repeat>
         </repeat>
@@ -235,8 +245,12 @@
 
                     <repeat name="expression">
                         <param name="counts" value="exp.tsv" ftype="tsv" />
-                        <param name="sample_name" value="Sample1_rep1" />
-                        <param name="replica_group" value="Sample1" />
+                        <repeat name="expression_replicas">
+                            <param name="replicas" value="1,2" />
+                        </repeat>
+                        <repeat name="expression_replicas_names">
+                            <param name="replica_names" value="ReplicaName1" />
+                        </repeat>
                         <param name="sample_description" value="Pointless experiment" />
                     </repeat>
                 </repeat>
@@ -246,7 +260,7 @@
                 <has_text text="addGenome succesfully inserted 1 elements" />
                 <has_text text="addAnnotation succesfully inserted 5 elements" />
                 <has_text text="addSimilarSequence succesfully inserted 1 elements" />
-                <has_text text="addTranscriptome succesfully inserted 1 elements" />
+                <has_text text="addExpression succesfully inserted 4 elements" />
             </assert_stdout>
         </test>
         <test>
@@ -272,8 +286,12 @@
 
                     <repeat name="expression">
                         <param name="counts" value="exp.tsv" ftype="tsv" />
-                        <param name="sample_name" value="Sample1_rep1" />
-                        <param name="replica_group" value="Sample1" />
+                        <repeat name="expression_replicas">
+                            <param name="replicas" value="1,2" />
+                        </repeat>
+                        <repeat name="expression_replicas_names">
+                            <param name="replica_names" value="ReplicaName1" />
+                        </repeat>
                         <param name="sample_description" value="Pointless experiment" />
                     </repeat>
                 </repeat>
@@ -283,7 +301,7 @@
                 <has_text text="addGenome succesfully inserted 1 elements" />
                 <has_text text="addAnnotation succesfully inserted 5 elements" />
                 <has_text text="addSimilarSequence succesfully inserted 1 elements" />
-                <has_text text="addTranscriptome succesfully inserted 1 elements" />
+                <has_text text="addExpression succesfully inserted 4 elements" />
             </assert_stdout>
         </test>
     </tests>
diff --git a/tools/genenotebook/macros.xml b/tools/genenotebook/macros.xml
index 5fd1a45..bfdbbe6 100644
--- a/tools/genenotebook/macros.xml
+++ b/tools/genenotebook/macros.xml
@@ -7,7 +7,7 @@
         </requirements>
     </xml>
 
-    <token name="@TOOL_VERSION@">0.4.5</token>
+    <token name="@TOOL_VERSION@">0.4.7</token>
     <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token>
 
     <xml name="citation">
diff --git a/tools/genenotebook/test-data/exp.tsv b/tools/genenotebook/test-data/exp.tsv
index e04dcad..42de3b8 100644
--- a/tools/genenotebook/test-data/exp.tsv
+++ b/tools/genenotebook/test-data/exp.tsv
@@ -1,2 +1,2 @@
-target_id	length	eff_length	est_counts	tpm
-MMUCEDO_000001-T1	1221	1021.99	21	1.80368
+gene	Sample1	Sample2	Sample3	Sample4
+MMUCEDO_000001-T1	1000	2000	3000	4000

From 72a16c1ddedd1d460fce05131de2a5a04d5baadb Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 29 Sep 2023 21:21:50 +0000
Subject: [PATCH 2/8] fix

---
 tools/genenotebook/genenotebook_build.xml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tools/genenotebook/genenotebook_build.xml b/tools/genenotebook/genenotebook_build.xml
index bbbc836..61395c7 100644
--- a/tools/genenotebook/genenotebook_build.xml
+++ b/tools/genenotebook/genenotebook_build.xml
@@ -58,14 +58,15 @@
 
         #for exp in $annot.expression:
                 genoboo add expression @CONNECT_INFO@
-                    #for replica in $exp.replicas:
+		    --sample-description '${exp.sample_description}'
+		    ${exp.public}
+                    #for replica in $exp.expression_replicas:
                         --replicas '${replica.replicas}'
                     #end for
                     #for replica_group_name in $exp.expression_replicas_names:
-                        --sample-description '${replica_group_name.replica_names}'
+                        --replica-names '${replica_group_name.replica_names}'
                     #end for
-                    --sample-description '${exp.sample_description}'
-                    '${exp.public}'
+                    --
                     '${exp.counts}';
         #end for
     #end for

From 6bd9e2968f59c0fd5dd628c214038c5d4f0c9c45 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 2 Oct 2023 07:53:37 +0000
Subject: [PATCH 3/8] more test

---
 tools/genenotebook/genenotebook_build.xml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/tools/genenotebook/genenotebook_build.xml b/tools/genenotebook/genenotebook_build.xml
index 61395c7..0f38ce2 100644
--- a/tools/genenotebook/genenotebook_build.xml
+++ b/tools/genenotebook/genenotebook_build.xml
@@ -246,13 +246,8 @@
 
                     <repeat name="expression">
                         <param name="counts" value="exp.tsv" ftype="tsv" />
-                        <repeat name="expression_replicas">
-                            <param name="replicas" value="1,2" />
-                        </repeat>
-                        <repeat name="expression_replicas_names">
-                            <param name="replica_names" value="ReplicaName1" />
-                        </repeat>
                         <param name="sample_description" value="Pointless experiment" />
+			<param name="public" value="true" />
                     </repeat>
                 </repeat>
             </repeat>
@@ -289,9 +284,11 @@
                         <param name="counts" value="exp.tsv" ftype="tsv" />
                         <repeat name="expression_replicas">
                             <param name="replicas" value="1,2" />
+                            <param name="replicas" value="3,4" />
                         </repeat>
                         <repeat name="expression_replicas_names">
                             <param name="replica_names" value="ReplicaName1" />
+                            <param name="replica_names" value="ReplicaName2" />
                         </repeat>
                         <param name="sample_description" value="Pointless experiment" />
                     </repeat>

From 57e163914a2872b095a6aacf2ad2aa9a86f7c242 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 2 Oct 2023 11:18:05 +0200
Subject: [PATCH 4/8] Merge repeat block

---
 tools/genenotebook/genenotebook_build.xml | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/tools/genenotebook/genenotebook_build.xml b/tools/genenotebook/genenotebook_build.xml
index 0f38ce2..25a2b58 100644
--- a/tools/genenotebook/genenotebook_build.xml
+++ b/tools/genenotebook/genenotebook_build.xml
@@ -62,9 +62,7 @@
 		    ${exp.public}
                     #for replica in $exp.expression_replicas:
                         --replicas '${replica.replicas}'
-                    #end for
-                    #for replica_group_name in $exp.expression_replicas_names:
-                        --replica-names '${replica_group_name.replica_names}'
+                        --replica-names '${replica.replica_names}'
                     #end for
                     --
                     '${exp.counts}';
@@ -129,11 +127,9 @@
                     <param name="counts" label="Expression data" optional="true" type="data" format="tsv" />
                     <repeat name="expression_replicas" title="Expression replicas">
                         <param argument="--replicas" name="replicas" label="Comma-separated replica column positions" type="text" help="Comma-separated column positions, which are part of the same replica group. Can be set multiple times for multiple groups. The replica group name will be the first column, unless replica-names is set" />
-                    </repeat>
-                    <repeat name="expression_replicas_names" title="Expression replicas">
                         <param argument="--replica-names" name="replica_names" label="Identifier to group samples that belong to the same experiment" type="text"  help="Name of the replica group. Will defaut to the first column header if not set. Can be set multiple time (for each replica group). Will match replica groups in order, whether they are multiple of single columns."/>
                     </repeat>
-                    <param argument="--sample-description" name="sample_description" label="Description of the experiment" type="text" help="Name of the replica group. Will defaut to the first column header if not set. Can be set multiple time (for each replica group). Will match replica groups in order, whether they are multiple or single columns." />
+                    <param argument="--sample-description" name="sample_description" label="Description of the experiment" />
                     <param name="public" label="Public access" type="boolean" truevalue="--public" falsevalue="" value="false" />
                 </repeat>
             </repeat>
@@ -247,7 +243,7 @@
                     <repeat name="expression">
                         <param name="counts" value="exp.tsv" ftype="tsv" />
                         <param name="sample_description" value="Pointless experiment" />
-			<param name="public" value="true" />
+                        <param name="public" value="true" />
                     </repeat>
                 </repeat>
             </repeat>
@@ -284,10 +280,10 @@
                         <param name="counts" value="exp.tsv" ftype="tsv" />
                         <repeat name="expression_replicas">
                             <param name="replicas" value="1,2" />
-                            <param name="replicas" value="3,4" />
-                        </repeat>
-                        <repeat name="expression_replicas_names">
                             <param name="replica_names" value="ReplicaName1" />
+                        </repeat>
+                        <repeat name="expression_replicas">
+                            <param name="replicas" value="3,4" />
                             <param name="replica_names" value="ReplicaName2" />
                         </repeat>
                         <param name="sample_description" value="Pointless experiment" />

From ac27e5e3cfccac83d9e6bc7c1a48e7e71deacc17 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 2 Oct 2023 11:26:52 +0200
Subject: [PATCH 5/8] typo

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

diff --git a/tools/genenotebook/genenotebook_build.xml b/tools/genenotebook/genenotebook_build.xml
index 25a2b58..c8270eb 100644
--- a/tools/genenotebook/genenotebook_build.xml
+++ b/tools/genenotebook/genenotebook_build.xml
@@ -129,7 +129,7 @@
                         <param argument="--replicas" name="replicas" label="Comma-separated replica column positions" type="text" help="Comma-separated column positions, which are part of the same replica group. Can be set multiple times for multiple groups. The replica group name will be the first column, unless replica-names is set" />
                         <param argument="--replica-names" name="replica_names" label="Identifier to group samples that belong to the same experiment" type="text"  help="Name of the replica group. Will defaut to the first column header if not set. Can be set multiple time (for each replica group). Will match replica groups in order, whether they are multiple of single columns."/>
                     </repeat>
-                    <param argument="--sample-description" name="sample_description" label="Description of the experiment" />
+                    <param argument="--sample-description" name="sample_description" label="Description of the experiment" type="text" />
                     <param name="public" label="Public access" type="boolean" truevalue="--public" falsevalue="" value="false" />
                 </repeat>
             </repeat>

From 4b15c1c5c425e4acb4d1b1dd897796bed4d1a5d1 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 10 Oct 2023 15:45:11 +0200
Subject: [PATCH 6/8] polish

---
 tools/genenotebook/genenotebook_build.xml | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/tools/genenotebook/genenotebook_build.xml b/tools/genenotebook/genenotebook_build.xml
index c8270eb..5723840 100644
--- a/tools/genenotebook/genenotebook_build.xml
+++ b/tools/genenotebook/genenotebook_build.xml
@@ -58,8 +58,8 @@
 
         #for exp in $annot.expression:
                 genoboo add expression @CONNECT_INFO@
-		    --sample-description '${exp.sample_description}'
-		    ${exp.public}
+                    --sample-description ''
+                    ${exp.public}
                     #for replica in $exp.expression_replicas:
                         --replicas '${replica.replicas}'
                         --replica-names '${replica.replica_names}'
@@ -124,13 +124,12 @@
                 </conditional>
 
                 <repeat name="expression" title="Expression data">
-                    <param name="counts" label="Expression data" optional="true" type="data" format="tsv" />
+                    <param name="counts" label="Expression data tabular file" help="One line per mRNA, first column is mRNA ID, each other columns is an experimental condition. TPM values preferably." optional="false" type="data" format="tsv" />
+                    <param name="public" label="Public access" type="boolean" truevalue="--public" falsevalue="" value="false" />
                     <repeat name="expression_replicas" title="Expression replicas">
-                        <param argument="--replicas" name="replicas" label="Comma-separated replica column positions" type="text" help="Comma-separated column positions, which are part of the same replica group. Can be set multiple times for multiple groups. The replica group name will be the first column, unless replica-names is set" />
-                        <param argument="--replica-names" name="replica_names" label="Identifier to group samples that belong to the same experiment" type="text"  help="Name of the replica group. Will defaut to the first column header if not set. Can be set multiple time (for each replica group). Will match replica groups in order, whether they are multiple of single columns."/>
+                        <param argument="--replica-names" label="Name of a replica group" type="text"/>
+                        <param argument="--replicas" label="Comma-separated list of columns of replicas (e.g. 1,2,3)" type="text" help="Comma-separated list of column positions, which are part of the same replica group. Columns not mentionned in any replica group will be considered to be a single replica experiment." />
                     </repeat>
-                    <param argument="--sample-description" name="sample_description" label="Description of the experiment" type="text" />
-                    <param name="public" label="Public access" type="boolean" truevalue="--public" falsevalue="" value="false" />
                 </repeat>
             </repeat>
         </repeat>
@@ -242,7 +241,6 @@
 
                     <repeat name="expression">
                         <param name="counts" value="exp.tsv" ftype="tsv" />
-                        <param name="sample_description" value="Pointless experiment" />
                         <param name="public" value="true" />
                     </repeat>
                 </repeat>
@@ -286,7 +284,6 @@
                             <param name="replicas" value="3,4" />
                             <param name="replica_names" value="ReplicaName2" />
                         </repeat>
-                        <param name="sample_description" value="Pointless experiment" />
                     </repeat>
                 </repeat>
             </repeat>

From ec665a05678cf84c2bb8471b5d3c274cfacda3b8 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 10 Oct 2023 15:53:44 +0200
Subject: [PATCH 7/8] add hectar (fixes #84)

---
 tools/genenotebook/genenotebook_build.xml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tools/genenotebook/genenotebook_build.xml b/tools/genenotebook/genenotebook_build.xml
index 5723840..0ce2b4c 100644
--- a/tools/genenotebook/genenotebook_build.xml
+++ b/tools/genenotebook/genenotebook_build.xml
@@ -40,6 +40,10 @@
             genoboo add eggnog @CONNECT_INFO@ '${annot.eggnog}';
         #end if
 
+        #if $annot.hectar:
+            genoboo add hectar @CONNECT_INFO@ '${annot.hectar}';
+        #end if
+
         #if $annot.blast_cond.blast_choice == "blast":
             genoboo add blast @CONNECT_INFO@
                 --format 'xml'
@@ -101,6 +105,7 @@
                 </conditional>
                 <param name="interproscan" label="InterProScan results" optional="true" type="data" format="tsv,gff3" />
                 <param name="eggnog" label="EggNOG-Mapper results" optional="true" type="data" format="tsv" />
+                <param name="hectar" label="Hectar results" optional="true" type="data" format="tsv" />
 
                 <conditional name="blast_cond">
                     <param name="blast_choice" type="select" label="Import Blast or Diamond results">

From b182dcca2a33938968435c3a881e12da6e4e4156 Mon Sep 17 00:00:00 2001
From: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Date: Tue, 10 Oct 2023 15:56:56 +0200
Subject: [PATCH 8/8] test for hectar

---
 tools/genenotebook/genenotebook_build.xml | 1 +
 tools/genenotebook/test-data/hectar.tsv   | 2 ++
 2 files changed, 3 insertions(+)
 create mode 100644 tools/genenotebook/test-data/hectar.tsv

diff --git a/tools/genenotebook/genenotebook_build.xml b/tools/genenotebook/genenotebook_build.xml
index 0ce2b4c..a358789 100644
--- a/tools/genenotebook/genenotebook_build.xml
+++ b/tools/genenotebook/genenotebook_build.xml
@@ -213,6 +213,7 @@
                     <param name="annotation" value="annot.gff" />
                     <param name="interproscan" value="interproscan.tsv" ftype="tsv" />
                     <param name="eggnog" value="eggnog.tsv" ftype="tsv" />
+                    <param name="hectar" value="hectar.tsv" ftype="tsv" />
                 </repeat>
             </repeat>
             <output name="gnb_db" file="output/genome_annot_ips_en.tar.bz2" compare="sim_size" delta="15000" />
diff --git a/tools/genenotebook/test-data/hectar.tsv b/tools/genenotebook/test-data/hectar.tsv
new file mode 100644
index 0000000..137b2ef
--- /dev/null
+++ b/tools/genenotebook/test-data/hectar.tsv
@@ -0,0 +1,2 @@
+protein id	predicted targeting category	signal peptide score	signal peptide cleavage site	type II signal anchor score	chloroplast score	mitochondrion score	other score
+MMUCEDO_000002-T1	other localisation	0.0583	-	0.0228	-	0.1032	0.8968