From 8393e9d92f985fe8f7b360dc69782587bae56b2f Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 23 Oct 2023 10:26:15 +0200
Subject: [PATCH] Release 0.4.8

---
 tools/genenotebook/genenotebook_build.xml | 11 ++++++++---
 tools/genenotebook/macros.xml             |  2 +-
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/tools/genenotebook/genenotebook_build.xml b/tools/genenotebook/genenotebook_build.xml
index a358789..aaa13fa 100644
--- a/tools/genenotebook/genenotebook_build.xml
+++ b/tools/genenotebook/genenotebook_build.xml
@@ -12,7 +12,7 @@
     genoboo add genome @CONNECT_INFO@ --name '${genome.name}' ${genome.public} '${genome.genome}';
 
     #for annot in $genome.annots:
-        genoboo add annotation @CONNECT_INFO@ --name '${genome.name}'
+        genoboo add annotation @CONNECT_INFO@ --name '${genome.name}' --annot '${annot.annot}'
         #if $annot.prot_naming.method == 'regex'
             #if $annot.prot_naming.re_protein:
             --re_protein '$annot.prot_naming.re_protein'
@@ -33,19 +33,21 @@
             #else:
                 tsv
             #end if
+            --annot '${annot.annot}'
             '${annot.interproscan}';
         #end if
 
         #if $annot.eggnog:
-            genoboo add eggnog @CONNECT_INFO@ '${annot.eggnog}';
+            genoboo add eggnog @CONNECT_INFO@ --annot '${annot.annot}' '${annot.eggnog}';
         #end if
 
         #if $annot.hectar:
-            genoboo add hectar @CONNECT_INFO@ '${annot.hectar}';
+            genoboo add hectar @CONNECT_INFO@ --annot '${annot.annot}' '${annot.hectar}';
         #end if
 
         #if $annot.blast_cond.blast_choice == "blast":
             genoboo add blast @CONNECT_INFO@
+                --annot '${annot.annot}'
                 --format 'xml'
                 --algorithm '${annot.blast_cond.algorithm}'
                 --matrix '${annot.blast_cond.matrix}'
@@ -53,6 +55,7 @@
                 '${annot.blast_cond.blast}';
         #elif $annot.blast_cond.blast_choice == "diamond":
             genoboo add diamond @CONNECT_INFO@
+                --annot '${annot.annot}'
                 --format 'xml'
                 --algorithm '${annot.blast_cond.algorithm}'
                 --matrix '${annot.blast_cond.matrix}'
@@ -62,6 +65,7 @@
 
         #for exp in $annot.expression:
                 genoboo add expression @CONNECT_INFO@
+                    --annot '${annot.annot}'
                     --sample-description ''
                     ${exp.public}
                     #for replica in $exp.expression_replicas:
@@ -84,6 +88,7 @@
             <param name="public" label="Public access" type="boolean" truevalue="--public" falsevalue="" value="false" />
             <repeat name="annots" title="Annotations">
                 <param name="annotation" label="Annotation" type="data" format="gff3" />
+                <param argument="--annot" label="Annotation name" type="text" help="Annotation name" />
                 <conditional name="prot_naming">
                     <param name="method" type="select" label="Protein naming method">
                         <option value="none">No specific names for proteins</option>
diff --git a/tools/genenotebook/macros.xml b/tools/genenotebook/macros.xml
index bfdbbe6..15e90be 100644
--- a/tools/genenotebook/macros.xml
+++ b/tools/genenotebook/macros.xml
@@ -7,7 +7,7 @@
         </requirements>
     </xml>
 
-    <token name="@TOOL_VERSION@">0.4.7</token>
+    <token name="@TOOL_VERSION@">0.4.8</token>
     <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token>
 
     <xml name="citation">