--- a/maker.xml	Tue Aug 31 09:19:55 2021 +0000
+++ b/maker.xml	Tue Feb 08 14:16:13 2022 +0000
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy@SUFFIX_VERSION@">
     <description>genome annotation pipeline</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <xrefs>
         <xref type="bio.tools">maker</xref>
     </xrefs>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <expand macro="requirements"/>
     <command><![CDATA[
         RM_PATH=\$(which RepeatMasker) &&
@@ -245,6 +245,12 @@
     </configfiles>
 
     <inputs>
+        <!-- More info on licensing in https://github.com/galaxyproject/iwc/pull/47#issuecomment-962260646 -->
+        <param name="license_agreement" type="boolean" label="Are you running Maker for academic use, or did you purchase a license?"
+            help="The MAKER authors specifically allowed to make it available on Galaxy. MAKER is free for academic use, but commercial Galaxy users of MAKER still need a license, which can be obtained at http://weatherby.genetics.utah.edu/cgi-bin/registration/maker_license.cgi">
+            <validator type="expression" message="You must either run Maker for academic use, or purchase a license.">value</validator>
+        </param>
+
         <param name="genome" type="data" format="fasta" label="Genome to annotate"/>
         <param name="organism_type" type="select" label="Organism type">
             <option value="eukaryotic">Eukaryotic</option>
@@ -302,7 +308,6 @@
                         <option value="human">Homo sapiens</option>
                         <option value="fly">Drosophila melanogaster</option>
                         <option value="arabidopsis">Arabidopsis thaliana</option>
-                        <option value="brugia ">Brugia malayi</option>
                         <option value="aedes">Aedes aegypti</option>
                         <option value="tribolium2012">Tribolium castaneum</option>
                         <option value="schistosoma">Schistosoma mansoni</option>
@@ -310,41 +315,38 @@
                         <option value="galdieria">Galdieria sulphuraria</option>
                         <option value="maize">Zea mays</option>
                         <option value="toxoplasma">Toxoplasma gondii</option>
-                        <option value="caenorhabditis ">Caenorhabditis elegans</option>
+                        <option value="caenorhabditis">Caenorhabditis elegans</option>
                         <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
-                        <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
-                        <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
+                        <option value="aspergillus_nidulans">Aspergillus nidulans</option>
+                        <option value="aspergillus_oryzae">Aspergillus oryzae</option>
                         <option value="aspergillus_terreus">Aspergillus terreus</option>
-                        <option value="botrytis_cinerea ">Botrytis cinerea</option>
-                        <option value="candida_albicans ">Candida albicans</option>
-                        <option value="candida_guilliermondii ">Candida guilliermondii</option>
-                        <option value="candida_tropicalis ">Candida tropicalis</option>
+                        <option value="botrytis_cinerea">Botrytis cinerea</option>
+                        <option value="candida_albicans">Candida albicans</option>
+                        <option value="candida_guilliermondii">Candida guilliermondii</option>
+                        <option value="candida_tropicalis">Candida tropicalis</option>
                         <option value="chaetomium_globosum">Chaetomium globosum</option>
                         <option value="coccidioides_immitis">Coccidioides immitis</option>
-                        <option value="coprinus">Coprinus cinereus</option>
                         <option value="coprinus_cinereus">Coprinus cinereus</option>
                         <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
-                        <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
-                        <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
-                        <option value="cryptococcus">Cryptococcus neoformans</option>
+                        <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans B</option>
+                        <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans JEC21</option>
                         <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
-                        <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
+                        <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi GB</option>
                         <option value="eremothecium_gossypii">Eremothecium gossypii</option>
-                        <option value="fusarium_graminearum ">Fusarium graminearum</option>
-                        <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
-                        <option value="histoplasma">Histoplasma capsulatum</option>
-                        <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
-                        <option value="laccaria_bicolor ">Laccaria bicolor</option>
+                        <option value="fusarium_graminearum">Fusarium graminearum</option>
+                        <option value="histoplasma_capsulatum">Histoplasma capsulatum</option>
+                        <option value="kluyveromyces_lactis">Kluyveromyces lactis</option>
+                        <option value="laccaria_bicolor">Laccaria bicolor</option>
                         <option value="lamprey">Petromyzon marinus</option>
                         <option value="leishmania_tarentolae">Leishmania tarentolae</option>
                         <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
-                        <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
+                        <option value="magnaporthe_grisea">Magnaporthe grisea</option>
                         <option value="neurospora_crassa">Neurospora crassa</option>
                         <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
                         <option value="pichia_stipitis">Pichia stipitis</option>
                         <option value="rhizopus_oryzae">Rhizopus oryzae</option>
-                        <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
-                        <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
+                        <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae S288C</option>
+                        <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae rm11-1a_1</option>
                         <option value="saccharomyces">Saccharomyces cerevisiae</option>
                         <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
                         <option value="trichinella">Trichinella spiralis</option>
@@ -367,25 +369,21 @@
                         <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
                         <option value="wheat">wheat</option>
                         <option value="zebrafish">Danio rerio</option>
-                        <option value="anidulans">Aspergillus nidulans</option>
                         <option value="bombus_impatiens1">Bombus impatiens1</option>
                         <option value="bombus_terrestris2">Bombus terrestris2</option>
-                        <option value="botrytis_cinerea">Botrytis cinerea</option>
                         <option value="brugia_malayi">Brugia malayi</option>
                         <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
                         <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
                         <option value="culex_pipiens">Culex pipiens</option>
                         <option value="elephant_shark">Callorhinchus milii</option>
                         <option value="honeybee1">Apis mellifera</option>
-                        <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
                         <option value="pea_aphid">Acyrthosiphon pisum</option>
                         <option value="rhodnius_prolixus">Rhodnius prolixus</option>
-                        <option value="ustilago_maydis">Ustilago maydis</option>
                         <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
                         <option value="verticillium_longisporum1">Verticillium longisporum1</option>
-                        <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
+                        <option value="Xipophorus_maculatus">Xipophorus maculatus</option>
                         <option value="adorsata">adorsata</option>
-                        <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
+                        <option value="ancylostoma_ceylanicum">Ancylostoma ceylanicum</option>
                         <option value="maker2_athal1">maker2_athal1</option>
                         <option value="maker2_c_elegans1">maker2_c_elegans1</option>
                         <option value="maker2_dmel1">maker2_dmel1</option>
@@ -492,6 +490,7 @@
     </outputs>
     <tests>
         <test>
+            <param name="license_agreement" value="true" />
             <param name="genome" value="genome.fasta"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
@@ -500,6 +499,7 @@
             <output name="output_evidences" file="evidences.gff3" compare="sim_size"/>
         </test>
         <test>
+            <param name="license_agreement" value="true" />
             <param name="genome" value="genome.fasta"/>
             <param name="organism_type" value="prokaryotic"/>
             <param name="est_evidences|est" value="est.fasta"/>
@@ -509,6 +509,7 @@
             <output name="output_evidences" file="evidences_proc.gff3" compare="sim_size"/>
         </test>
         <test>
+            <param name="license_agreement" value="true" />
             <param name="genome" value="genome.fasta"/>
             <param name="reannotation|reannotate" value="yes"/>
             <param name="reannotation|maker_gff" value="evidences.gff3"/>
@@ -519,6 +520,7 @@
             <output name="output_evidences" file="evidences_reuse.gff3" compare="sim_size"/>
         </test>
         <test>
+            <param name="license_agreement" value="true" />
             <param name="genome" value="genome.fasta"/>
             <param name="abinitio_gene_prediction|snaphmm" value="snap.hmm"/>
             <param name="abinitio_gene_prediction|aug_prediction|augustus_mode" value="builtin"/>
@@ -530,6 +532,7 @@
             <output name="output_evidences" file="evidences_human.gff3" compare="sim_size"/>
         </test>
         <test>
+            <param name="license_agreement" value="true" />
             <param name="genome" value="genome.fasta"/>
             <param name="abinitio_gene_prediction|snaphmm" value="snap.hmm"/>
             <param name="abinitio_gene_prediction|aug_prediction|augustus_mode" value="history"/>
@@ -541,6 +544,7 @@
             <output name="output_evidences" file="evidences_model.gff3" compare="sim_size"/>
         </test>
         <test>
+            <param name="license_agreement" value="true" />
             <param name="genome" value="genome.fasta"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
@@ -549,6 +553,7 @@
             <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
         </test>
         <test>
+            <param name="license_agreement" value="true" />
             <param name="genome" value="genome.fasta"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
@@ -558,6 +563,7 @@
             <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
         </test>
         <test>
+            <param name="license_agreement" value="true" />
             <param name="genome" value="genome.fasta"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
@@ -568,6 +574,7 @@
             <output name="output_evidences" file="evidences_norm_dfam_up.gff3" compare="sim_size"/>
         </test>
         <test>
+            <param name="license_agreement" value="true" />
             <param name="genome" value="genome.fasta"/>
             <param name="est_evidences|est" value="non_IUPAC.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>