Main mutable configs

galaxyproject · Apr 30, 2020 · a1e2241 · a1e2241
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diff --git a/env/main/files/galaxy/var/integrated_tool_panel.xml b/env/main/files/galaxy/var/integrated_tool_panel.xml
@@ -345,6 +345,8 @@
 
     <section id="fasta_fastq" name="FASTA/FASTQ" version="">
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fasta_concatenate_by_species/fasta_concatenate0/0.0.1" />
@@ -1875,6 +1877,10 @@
 
     <section id="annotation" name="Annotation" version="">
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate_list/1.0.1" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/exonerate/exonerate/2.4.0+galaxy2" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/tetyper/tetyper/1.1+galaxy1" />
@@ -2587,6 +2593,10 @@
 
     <section id="multiple_alignments" name="Multiple Alignments" version="">
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/0.1.7" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/0.1.6" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/0.1.5" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/0.1.4" />
@@ -4781,6 +4791,54 @@
 
     <section id="hyphy" name="HyPhy" version="">
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_sm19/hyphy_sm19/2.5.11+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_slac/hyphy_slac/2.5.11+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.11+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_prime/hyphy_prime/2.5.11+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_meme/hyphy_meme/2.5.11+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_gard/hyphy_gard/2.5.11+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.11+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.11+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fade/hyphy_fade/2.5.11+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_busted/hyphy_busted/2.5.11+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_bgm/hyphy_bgm/2.5.11+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_absrel/hyphy_absrel/2.5.11+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_sm19/hyphy_sm19/2.5.9+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_slac/hyphy_slac/2.5.9+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.9+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_prime/hyphy_prime/2.5.9+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_meme/hyphy_meme/2.5.9+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_gard/hyphy_gard/2.5.9+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.9+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.9+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fade/hyphy_fade/2.5.9+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_busted/hyphy_busted/2.5.9+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_bgm/hyphy_bgm/2.5.9+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_absrel/hyphy_absrel/2.5.9+galaxy0" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_sm19/hyphy_sm19/2.5.8+galaxy0" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hyphy_slac/hyphy_slac/2.5.8+galaxy0" />
@@ -5501,6 +5559,12 @@
 
     <section id="graph_display_data" name="Graph/Display Data" version="">
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.8+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.2" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.8+galaxy0" />
@@ -5877,4 +5941,14 @@
 
     <tool id="echo_main_bridges" />
 
+    <section id="getext" name="Get Data" version="">
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy2" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.4+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.4+galaxy1" />
+
+    </section>
+
 </toolbox>