--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PrepExternalSchema.xml	Wed Sep 25 14:13:01 2024 +0000
@@ -0,0 +1,55 @@
+<tool id="chewbbaca_prepexternalschema" name="chewBBACA PrepExternalSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Adapt an external schema to be used with chewBBACA</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        unzip '$input_schema' -d 'schema' &&
+        chewBBACA.py PrepExternalSchema
+            #if $training_file:
+                --ptf '$training_file'
+            #end if
+            #if $genes_list:
+                --gl '$genes_list'
+            #end if    
+            @COMMON_INPUT@
+            $size_filter
+            -g 'schema/' -o 'schema_seed' &&
+        zip -r PExternalschema_seed.zip 'schema_seed'
+    ]]></command>
+    <inputs>
+        <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and the schema must contain one FASTA file per gene/locus."/>
+        <section name="advanced" title="Advanced options">
+            <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
+            <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" />
+            <param argument="--minimum-length" type="integer" min="0" value="0" label="Minimum sequence length value"/>
+            <expand macro="common_param" />
+            <param argument="--size-filter" type="boolean" truevalue="--size-filter" falsevalue="" checked="false" label="Size filter" help="Apply the minimum length and size threshold values to filter out alleles during schema adaptation" />
+        </section>
+    </inputs>
+    <outputs>
+        <data format="zip" name="schema" from_work_dir="PExternalschema_seed.zip" label="${tool.name} on ${on_string}: PrepExternal Schema files"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_schema" value="PrepExternal_test.zip"/>
+            <param name="size_filter" value="false"/>
+            <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>
+    </tests>
+    <help>
+        
+chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
+
+The PrepExternalSchema module enables the adaptation of external schemas so that it is possible to use those schemas with chewBBACA.
+
+    </help>
+    <expand macro="citations" />
+</tool>