# HG changeset patch
# User iuc
# Date 1717770446 0
# Node ID 6a8df4d75f3ab97f30bef2f222b650cb32136523
# Parent  220e2f7ff8bb7b27edee1c8145d5fd21ebece1f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 501c1cb91f4b91ec93e6df6e555323bbe8e2b703

diff -r 220e2f7ff8bb -r 6a8df4d75f3a CreateSchema.xml
--- a/CreateSchema.xml	Sat May 11 22:50:19 2024 +0000
+++ b/CreateSchema.xml	Fri Jun 07 14:27:26 2024 +0000
@@ -5,9 +5,11 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
+        #import re
         mkdir 'input' &&
         #for $file in $input_file
-        ln -sf '$file' 'input/${file.element_identifier}' &&
+        #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($file.element_identifier))
+        ln -sf '$file' 'input/${escaped_element_identifier}.${file.ext}' &&
         #end for
         chewBBACA.py CreateSchema 
             #if $training_file:
@@ -62,6 +64,16 @@
             </output>
         </test>
         <test expect_num_outputs="1">
+            <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic"/>
+            <output name="schema">
+                <assert_contents>
+                    <has_archive_member path="schema_seed/.*\.fasta" n="204"/>
+                    <has_archive_member path="schema_seed/short/.*\.fasta" n="102"/>
+                    <has_archive_member path="schema_seed/\.schema_config"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
             <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
             <param name="training_file" value="Streptococcus_agalactiae.trn"/>
             <output name="schema">
@@ -77,7 +89,7 @@
             <param name="cds_input" value="true"/>
             <output name="schema">
                 <assert_contents>
-                    <has_archive_member path="schema_seed/CDS-Str-agalactiae-protein1.fasta"/>
+                    <has_archive_member path="schema_seed/CDS-Str-agalactiae-fasta-protein1.fasta"/>
                 </assert_contents>
             </output>
         </test>
diff -r 220e2f7ff8bb -r 6a8df4d75f3a macros.xml
--- a/macros.xml	Sat May 11 22:50:19 2024 +0000
+++ b/macros.xml	Fri Jun 07 14:27:26 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 220e2f7ff8bb -r 6a8df4d75f3a test-data/PrepExternal_test.zip
Binary file test-data/PrepExternal_test.zip has changed