# HG changeset patch
# User iuc
# Date 1717770437 0
# Node ID 0b73dd40d83f037796bd08a89d1ca5e9dd121e84
# Parent  7035fc8b4ae3e14149b5b6fdcfb47a0b50419a7d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 501c1cb91f4b91ec93e6df6e555323bbe8e2b703

diff -r 7035fc8b4ae3 -r 0b73dd40d83f PrepExternalSchema.xml
--- a/PrepExternalSchema.xml	Sat May 11 22:49:51 2024 +0000
+++ b/PrepExternalSchema.xml	Fri Jun 07 14:27:17 2024 +0000
@@ -5,7 +5,6 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir 'schema' &&
         unzip '$input_schema' -d 'schema' &&
         chewBBACA.py PrepExternalSchema
             #if $training_file:
@@ -16,11 +15,11 @@
             #end if    
             @COMMON_INPUT@
             $size_filter
-            -g 'schema/schema_seed/' -o 'schema_seed' &&
+            -g 'schema/' -o 'schema_seed' &&
         zip -r PExternalschema_seed.zip 'schema_seed'
     ]]></command>
     <inputs>
-        <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
+        <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and the schema must contain one FASTA file per gene/locus."/>
         <section name="advanced" title="Advanced options">
             <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
             <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" />
@@ -34,7 +33,7 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
+            <param name="input_schema" value="PrepExternal_test.zip"/>
             <param name="size_filter" value="false"/>
             <output name="schema">
                 <assert_contents>
diff -r 7035fc8b4ae3 -r 0b73dd40d83f macros.xml
--- a/macros.xml	Sat May 11 22:49:51 2024 +0000
+++ b/macros.xml	Fri Jun 07 14:27:17 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@CHEW_VERSION@">3.3.3</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="requirements">
         <requirements>
diff -r 7035fc8b4ae3 -r 0b73dd40d83f test-data/PrepExternal_test.zip
Binary file test-data/PrepExternal_test.zip has changed