From c9161d11d5debadd938a017be09a3d9e367ef14d Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Tue, 2 Jan 2024 22:50:04 +0100
Subject: [PATCH] add hidden giessen tools

---
 templates/galaxy/config/tool_conf.xml.j2 | 70 +++++++++++++-----------
 1 file changed, 39 insertions(+), 31 deletions(-)

diff --git a/templates/galaxy/config/tool_conf.xml.j2 b/templates/galaxy/config/tool_conf.xml.j2
index e9549b145..bd7f55427 100644
--- a/templates/galaxy/config/tool_conf.xml.j2
+++ b/templates/galaxy/config/tool_conf.xml.j2
@@ -447,8 +447,7 @@
     <tool file="/opt/galaxy/custom-tools/tombo/tombo_text_output.xml" labels="alpha" />
     <tool file="/opt/galaxy/custom-tools/tombo/tombo_detect_modifications.xml" labels="alpha" />
     <tool file="/opt/galaxy/custom-tools/tombo/tombo_plot_most_significant.xml" labels="alpha" />
-    <tool file="/opt/galaxy/custom-tools/tombo/tombo_plot_genome_locations.xml" labels="alpha" />	  
-	  
+    <tool file="/opt/galaxy/custom-tools/tombo/tombo_plot_genome_locations.xml" labels="alpha" />
     <tool file="/opt/galaxy/custom-tools/test/tpp/peptide_prophet.xml"  labels="beta" />
     <tool file="/opt/galaxy/custom-tools/test/tpp/pepxml_and_protxml_to_table.xml" />
     <tool file="/opt/galaxy/custom-tools/test/tpp/protein_prophet.xml"  />
@@ -559,12 +558,12 @@
         <tool file="interactive/interactivetool_source.xml" />
         <tool file="interactive/interactivetool_tadviewer.xml" />
         <tool file="interactive/interactivetool_qgis.xml" />
-	<tool file="interactive/interactivetool_qupath.xml" />
-    	<tool file="interactive/interactivetool_pampa.xml" />
+        <tool file="interactive/interactivetool_qupath.xml" />
+        <tool file="interactive/interactivetool_pampa.xml" />
         <tool file="interactive/interactivetool_odv.xml" />
         <tool file="interactive/interactivetool_ilastik.xml" />
         <tool file="interactive/interactivetool_metashrimps.xml" />
-  	<tool file="interactive/interactivetool_hdfview.xml" />
+        <tool file="interactive/interactivetool_hdfview.xml" />
         <tool file="interactive/interactivetool_scoop3.xml" />
         <tool file="interactive/interactivetool_divand.xml" />
         <tool file="interactive/interactivetool_blobtoolkit.xml" />
@@ -580,36 +579,45 @@
         <tool file="interactive/interactivetool_pangeo_ml_notebook.xml" />
         <tool file="interactive/interactivetool_rstudio.xml" />
         <tool file="interactive/interactivetool_rstudio_0_3.xml" />
-	<tool file="interactive/interactivetool_pyiron.xml" />
-	<tool file="interactive/interactivetool_higlass.xml" /> 
-	<tool file="interactive/interactivetool_openrefine.xml" />
+        <tool file="interactive/interactivetool_pyiron.xml" />
+        <tool file="interactive/interactivetool_higlass.xml" /> 
+        <tool file="interactive/interactivetool_openrefine.xml" />
         <tool file="interactive/interactivetool_panoply.xml" />
-	<tool file="interactive/interactivetool_askomics.xml" />
-	<tool file="interactive/interactivetool_cellxgene.xml" />
-	<tool file="interactive/interactivetool_cellxgene_1.1.1.xml" />
-	<tool file="interactive/interactivetool_bam_iobio.xml" />
-	<tool file="interactive/interactivetool_vcf_iobio.xml" />	
-	<tool file="interactive/interactivetool_neo4j.xml" />
-	<tool file="interactive/interactivetool_phinch.xml" />
-	<tool file="interactive/interactivetool_paraview.xml" />
-	<tool file="interactive/interactivetool_askomics.xml" />
-	<tool file="interactive/interactivetool_wilson.xml" />
-	<tool file="interactive/interactivetool_wallace.xml" />
-	<tool file="interactive/interactivetool_geoexplorer.xml" />
-	<tool file="interactive/interactivetool_radiant.xml" />
-	<tool file="interactive/interactivetool_ethercalc.xml" />
-	<tool file="interactive/interactivetool_vrm_editor.xml" />
-	<tool file="interactive/interactivetool_simtext_app.xml" />
-	<tool file="interactive/interactivetool_isee.xml" />
-	<tool file="interactive/interactivetool_metashark.xml" labels="beta" />
-	<tool file="interactive/interactivetool_audiolabeler.xml" />
- 	<tool file="interactive/interactivetool_genenotebook.xml" />
+        <tool file="interactive/interactivetool_askomics.xml" />
+        <tool file="interactive/interactivetool_cellxgene.xml" />
+        <tool file="interactive/interactivetool_cellxgene_1.1.1.xml" />
+        <tool file="interactive/interactivetool_bam_iobio.xml" />
+        <tool file="interactive/interactivetool_vcf_iobio.xml" />	
+        <tool file="interactive/interactivetool_neo4j.xml" />
+        <tool file="interactive/interactivetool_phinch.xml" />
+        <tool file="interactive/interactivetool_paraview.xml" />
+        <tool file="interactive/interactivetool_askomics.xml" />
+        <tool file="interactive/interactivetool_wilson.xml" />
+        <tool file="interactive/interactivetool_wallace.xml" />
+        <tool file="interactive/interactivetool_geoexplorer.xml" />
+        <tool file="interactive/interactivetool_radiant.xml" />
+        <tool file="interactive/interactivetool_ethercalc.xml" />
+        <tool file="interactive/interactivetool_vrm_editor.xml" />
+        <tool file="interactive/interactivetool_simtext_app.xml" />
+        <tool file="interactive/interactivetool_isee.xml" />
+        <tool file="interactive/interactivetool_metashark.xml" labels="beta" />
+        <tool file="interactive/interactivetool_audiolabeler.xml" />
+        <tool file="interactive/interactivetool_genenotebook.xml" />
         <tool file="interactive/interactivetool_holoviz.xml" />
-        <tool file="interactive/interactivetool_copernicus.xml" />  
+        <tool file="interactive/interactivetool_copernicus.xml" />
+    </section>
+
+  <section id="hidden_giessen_tools" name="Hidden Giessen Tools" >
+    <tool file="/opt/galaxy/custom-tools/giessen_tools/demultiplex_amplicons/demultiplex_by_primers.xml" hidden="True"/>
+    <tool file="/opt/galaxy/custom-tools/giessen_tools/index_read_filter/index_read_filter.xml" hidden="True"/>
+    <tool file="/opt/galaxy/custom-tools/giessen_tools/mOTU_table_generator/mOTU_table_generator.xml" hidden="True"/>
+    <tool file="/opt/galaxy/custom-tools/giessen_tools/motu_abundance_matrix/motu_abundance_matrix.xml" hidden="True"/>
+    <tool file="/opt/galaxy/custom-tools/giessen_tools/readname_changer/readname_changer.xml" hidden="True"/>
+    <tool file="/opt/galaxy/custom-tools/giessen_tools/trim_fasta_header/trim_fasta_header.xml" hidden="True"/>
   </section>
-  
+
 <!-- Earth-system subdomain -->
-<label id="earth-system-label-interactive-tools" text="General interactive tools" />  
+  <label id="earth-system-label-interactive-tools" text="General interactive tools" />  
   <section id="earth-system-section-interactivetools" name="Interactive tools">
     <tool file="interactive/interactivetool_jupyter_notebook.xml" />
     <tool file="interactive/interactivetool_jupyter_notebook_1.0.0.xml" />