# HG changeset patch
# User iuc
# Date 1728041508 0
# Node ID 22127ef4695bc36f9c1c370821f20503c30b1bcf
# Parent  912f9476dec8859d0788e4366bfade0b1520abb4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4

diff -r 912f9476dec8 -r 22127ef4695b augustus.xml
--- a/augustus.xml	Mon Aug 30 21:43:05 2021 +0000
+++ b/augustus.xml	Fri Oct 04 11:31:48 2024 +0000
@@ -1,11 +1,11 @@
-<tool id="augustus" name="Augustus" profile="20.01" version="@VERSION@+galaxy@SUFFIX_VERSION@">
+<tool id="augustus" name="Augustus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>gene prediction for prokaryotic and eukaryotic genomes</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <xrefs>
         <xref type="bio.tools">augustus</xref>
     </xrefs>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
 <![CDATA[
@@ -100,11 +100,11 @@
     </command>
     <inputs>
         <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
-        <param name="noInFrameStop" argument="--noInFrameStop" type="boolean"
+        <param argument="--noInFrameStop" type="boolean"
             label="Don't report transcripts with in-frame stop codons"
             truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false"
             help="Otherwise, intron-spanning stop codons could occur." />
-        <param name="singlestrand" type="boolean" argument="--singlestrand"
+        <param type="boolean" argument="--singlestrand"
             label="Predict genes independently on each strand"
             help="This allows overlapping genes on opposite strands."
             truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
@@ -121,16 +121,17 @@
                 <option value="history">Run Augustus with a custom trainingset</option>
             </param>
             <when value="history">
-                <param name="custom_model" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/>
+                <param name="custom_model" argument="--species" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/>
             </when>
             <when value="builtin">
-                <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
+                <param name="organism" argument="--species" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
                     <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) -->
                     <option value="human">Homo sapiens</option>
                     <option value="fly">Drosophila melanogaster</option>
                     <option value="maker2_dmel1">Drosophila melanogaster (maker2_dmel1)</option>
                     <option value="arabidopsis">Arabidopsis thaliana</option>
-                    <option value="brugia ">Brugia malayi</option>
+                    <option value="brugia">Brugia malayi (brugia)</option>
+                    <option value="brugia_malayi">Brugia malayi (brugia_malayi)</option>
                     <option value="aedes">Aedes aegypti</option>
                     <option value="tribolium2012">Tribolium castaneum</option>
                     <option value="schistosoma">Schistosoma mansoni</option>
@@ -139,45 +140,47 @@
                     <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="anidulans">Aspergillus nidulans (anidulans)</option>
+                    <option value="aspergillus_nidulans">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="coprinus">Coprinus cinereus (coprinus)</option>
+                    <option value="coprinus_cinereus">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="cryptococcus">Cryptococcus neoformans (cryptococcus)</option>
+                    <option value="cryptococcus_neoformans">Cryptococcus neoformans (cryptococcus_neoformans)</option>
                     <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
-                    <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
+                    <option value="Encephalitozoon_cuniculi">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 (histoplasma_capsulatum)</option>
+                    <option value="histoplasma">Histoplasma capsulatum (histoplasma)</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">Saccharomyces cerevisiae</option>
+                    <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae saccharomyces_cerevisiae_S288C</option>
+                    <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae RM11-1a-1</option>
+                    <option value="saccharomyces">Saccharomyces cerevisiae (saccharomyces)</option>
                     <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
                     <option value="trichinella">Trichinella spiralis</option>
-                    <option value="ustilago_maydis">Ustilago maydis</option>
                     <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
                     <option value="nasonia">Nasonia vitripennis</option>
                     <option value="tomato">Solanum lycopersicum</option>
@@ -196,17 +199,12 @@
                     <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
                     <option value="wheat">Triticum aestivum</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>
@@ -230,7 +228,6 @@
                     <option value="Trichoplax_adhaerens">Trichoplax adhaerens</option>
                     <option value="Aurelia_aurita">Aurelia aurita</option>
                     <option value="Rhopilema_esculentum">Rhopilema esculentum</option>
-                    <option value="Encephalitozoon_cuniculi">Encephalitozoon cuniculi</option>
                     <option value="Gonapodya_prolifera">Dunaliella salina</option>
                     <option value="Sordaria_macrospora">Sordaria macrospora</option>
                     <option value="Sphaceloma_murrayae">Sphaceloma murrayae</option>
@@ -253,20 +250,20 @@
             </when>
         </conditional>
 
-        <param name="softmasking" type="boolean" argument="--softmasking"
+        <param type="boolean" argument="--softmasking"
         label="Softmasking"
         truevalue="1" falsevalue="0" checked="true"
         help="If this option is enabled, lowercase letters are considered as repeated regions." />
 
 
-        <param name="strand" type="select" argument="--strand"
+        <param type="select" argument="--strand"
             label="Predict genes on specific strands">
             <option value="both">both</option>
             <option value="forward">forward</option>
             <option value="backward">backward</option>
         </param>
 
-        <param name="genemodel" label="Gene Model" type="select"
+        <param argument="--genemodel" label="Gene Model" type="select"
             help="Gene Model to predict, for more information please refer to the help.">
             <option value="complete">complete</option>
             <option value="partial">partial</option>
@@ -281,10 +278,10 @@
                 <option value="T">Yes</option>
             </param>
             <when value="T">
-                <param name="hintsfile" label="Select hints file from history" type="data" format="gff"
-                    help="A file containing hints in gff format (--hintsfile)"/>
-                <param name="extrinsiccfg" label="Select extrinsic configuration file from history" type="data" format="txt"
-                    help="A .cfg file listing hint sources and their boni and mali (--extrinsicCfgFile)"/>
+                <param argument="--hintsfile" label="Select hints file from history" type="data" format="gff"
+                    help="A file containing hints in gff format"/>
+                <param name="extrinsiccfg" argument="--extrinsicCfgFile" label="Select extrinsic configuration file from history" type="data" format="txt"
+                    help="A .cfg file listing hint sources and their boni and mali"/>
             </when>
             <when value="F">
             </when>
@@ -296,16 +293,16 @@
                 <option value="T">Yes</option>
             </param>
             <when value="T">
-                <param name="start" label="Starting position" type="integer" value=""
-                    help="The beginning of the search range (--predictionStart)"/>
-                <param name="stop" label="Ending position" type="integer" value=""
-                    help="The end of the search range (--predictionEnd); must be greater than starting position"/>
+                <param name="start" argument="--predictionStart" label="Starting position" type="integer" value=""
+                    help="The beginning of the search range"/>
+                <param name="stop" argument="--predictionEnd" label="Ending position" type="integer" value=""
+                    help="The end of the search range; must be greater than starting position"/>
             </when>
             <when value="F">
             </when>
         </conditional>
 
-        <param name="gff" type="boolean" label="GFF formated output"
+        <param name="gff" argument="--gff3" type="boolean" label="GFF formated output"
             help="Standard output is GTF."
             truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
 
@@ -332,14 +329,14 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
             <param name="organism" value="human" />
             <param name="utr" value="True" />
             <param name="softmasking" value="False"/>
             <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
             <param name="organism" value="human" />
             <param name="utr" value="True" />
@@ -347,7 +344,7 @@
             <param name="softmasking" value="False"/>
             <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
             <param name="organism" value="human" />
             <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />
@@ -356,7 +353,7 @@
             <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
             <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
             <param name="organism" value="fly" />
             <param name="usehints" value="T" />
@@ -364,6 +361,7 @@
             <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
             <param name="outputs" value="" />
             <param name="softmasking" value="False"/>
+            <param name="outputs" value=""/>
             <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12">
                 <assert_contents>
                     <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" />
@@ -372,7 +370,7 @@
             </output>
 
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
             <param name="organism" value="fly" />
             <param name="usehints" value="T" />
@@ -383,6 +381,7 @@
             <param name="stop" value="9000" />
             <param name="outputs" value="" />
             <param name="softmasking" value="False"/>
+            <param name="outputs" value=""/>
             <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12">
                 <assert_contents>
                     <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" />
@@ -391,11 +390,12 @@
             </output>
         </test>
         <!-- Test softmasking parameter-->
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
             <param name="organism" value="human" />
             <param name="utr" value="True" />
             <param name="softmasking" value="True"/>
+            <param name="outputs" value=""/>
             <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/>
         </test>
 
diff -r 912f9476dec8 -r 22127ef4695b macros.xml
--- a/macros.xml	Mon Aug 30 21:43:05 2021 +0000
+++ b/macros.xml	Fri Oct 04 11:31:48 2024 +0000
@@ -2,13 +2,14 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">augustus</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">augustus</requirement>
             <yield />
         </requirements>
     </xml>
 
-    <token name="@VERSION@">3.4.0</token>
-    <token name="@SUFFIX_VERSION@">1</token>
+    <token name="@TOOL_VERSION@">3.4.0</token>
+    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@PROFILE@">23.1</token>
 
 
     <xml name="citations">