diff funannotate_predict.xml @ 13:3e13e35ef26b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4

--- a/funannotate_predict.xml	Wed Jun 26 09:39:31 2024 +0000
+++ b/funannotate_predict.xml	Fri Mar 07 22:35:08 2025 +0000
@@ -21,8 +21,15 @@
     ## Need to copy too as the test_data is read only on CI
     cp -r '${database.fields.path}' './hacked_database' &&
     sed -i.bak 's|/tmp/prout|'`pwd`'/hacked_database|' './hacked_database/trained_species/fly/info.json' &&
+    #set db_path='$(pwd)/hacked_database'
+#else
+    #set db_path=$database.fields.path
 #end if
 
+## show detailed info about the reference DB on stdout
+export FUNANNOTATE_DB="$db_path" &&
+funannotate database &&
+
 mkdir -p input/ &&
 ln -s '${input}' input/input.fasta &&
 
@@ -30,11 +37,7 @@
 --input input/input.fasta
 --out output
 --tmpdir "\${_GALAXY_JOB_TMP_DIR:-/tmp}"
-#if $uglyTestingHack == "true":
-    --database `pwd`'/hacked_database'
-#else
-    --database '$database.fields.path'
-#end if
+--database "$db_path"
 
 $force
 
@@ -49,9 +52,9 @@
 --numbering ${organism.numbering}
 --header_length ${header_length}
 
-#if $parameters:
-    --parameters '${parameters}'
-#end if
+## #if $parameters:
+##     --parameters '${parameters}'
+## #end if
 
 #if $evidences.rna_bam
     --rna_bam ${evidences.rna_bam}
@@ -81,7 +84,7 @@
 --busco_seed_species '${busco.busco_seed_species}'
 --busco_db '${busco.busco_db}'
 
-#if $augustus.augustus_species != 'none':
+#if $augustus.augustus_species:
     --augustus_species '${augustus.augustus_species}'
 #end if
 --min_training_models ${augustus.min_training_models}
@@ -147,7 +150,7 @@
                 <column name="value" index="0" />
                 <column name="name" index="1" />
                 <column name="path" index="3" />
-                <filter type="sort_by" column="0" />
+                <filter type="sort_by" column="0" reverse_sort_order="true"/>
                 <filter type="static_value" column="2" value="1.0" />
             </options>
         </param>
@@ -193,14 +196,16 @@
                 <expand macro="busco_species"/>
             </param>
             <param argument="--busco_seed_species" type="select" label="Initial Augustus species training set for BUSCO alignment" help="Used when BUSCO runs Augustus internally.">
-                <expand macro="augustus_species"/>
+                <expand macro="busco_seeds">
+                    <filter type="add_value" value="anidulans" name="Anidulans" index="0"/> <!-- this sets the default -->
+                </expand>
             </param>
         </section>
 
         <section name="filtering" expanded="true" title="Filtering">
-            <param argument="--min_intronlen" type="integer" value="10" label="Minimum intron length" />
-            <param argument="--max_intronlen" type="integer" value="3000" label="Maximum intron length" />
-            <param argument="--min_protlen" type="integer" value="50" label="Minimum protein length" />
+            <param argument="--min_intronlen" type="integer" value="10" min="0" label="Minimum intron length" />
+            <param argument="--max_intronlen" type="integer" value="3000" min="0"  label="Maximum intron length" />
+            <param argument="--min_protlen" type="integer" value="50" min="0" label="Minimum protein length" />
             <param argument="--keep_no_stops" type="boolean" checked="false" truevalue="--keep_no_stops" falsevalue="" label="Keep gene models without valid stops" />
             <param argument="--repeat_filter" type="select" label="Repetitive gene model filtering" help="'overlap' drops gene models that are more than 90% contained within a repeat region; 'blast' compares the amino acid sequences to a small database of known transposons">
                 <option value="overlap blast" selected="True">overlap + blast</option>
@@ -210,12 +215,11 @@
             </param>
         </section>
 
-        <param argument="--parameters" type="data" format="json" optional="true" label="Ab-initio training parameters from a previous run" help="If specified, will over-rule any other training presets based on sepcies selection." />
+        <!-- <param argument="\-\-parameters" type="data" format="json" optional="true" label="Ab-initio training parameters from a previous run" help="If specified, will over-rule any other training presets based on sepcies selection." /> -->
 
         <section name="augustus" expanded="false" title="Augustus settings (advanced)">
-            <param argument="--augustus_species" type="select" label="Augustus species training set" help="Select a species from the list">
-                <option value="none" selected="True">No corresponding species, train from scratch</option>
-                <expand macro="augustus_species"/>
+            <param argument="--augustus_species" type="select" optional="true" label="Augustus species training set" help="Select a species from the list, use species name if empty">
+                <expand macro="busco_seeds"/>
             </param>
             <param argument="--min_training_models" type="integer" value="200" label="Minimum number of models to train Augustus" />
             <param argument="--optimize_augustus" type="boolean" checked="false" truevalue="--optimize_augustus" falsevalue="" label="Run 'optimize_augustus.pl' to refine training (long runtime)" />