--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hal_maf2hal.xml	Fri Feb 06 10:37:03 2026 +0000
@@ -0,0 +1,143 @@
+<tool id="hal_maf2hal" name="maf2hal" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>imports MAF into HAL database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/> 
+    <expand macro="stdio"/>
+    <command detect_errors="aggressive">
+        <![CDATA[
+        #if $mode.append == 'true':
+            ## If an input HAL file is provided to append to, ensure that it is not modified.
+            cp '$mode.input_hal' writable_hal.hal && 
+        #end if
+        ## Uncompress input
+        #if $input_maf.ext.endswith('.gz'):
+            gunzip -c '$input_maf' > uncompressed_input.maf &&
+        #else if $input_maf.ext.endswith('.bz2'):
+            bunzip2 -c '$input_maf' > uncompressed_input.maf &&
+        #else
+            cp '$input_maf' uncompressed_input.maf &&
+        #end if
+        maf2hal
+            #if $refGenome:
+                --refGenome '$refGenome'
+            #end if
+            #if $targetGenomes:
+                --targetGenomes '$targetGenomes'
+            #end if
+            #if $mode.append == 'true':
+                --append
+            #else if $mode.backend.format == 'mmap':
+                --format 'mmap'
+                --mmapFileSize $mode.backend.mmapFileSize
+            #end if
+            uncompressed_input.maf writable_hal.hal 
+    ]]></command>
+    <inputs>
+        <param name="input_maf" type="data" format="maf,maf.gz,maf.bz2" label="MAF file"/>
+        <param argument="--refGenome" type="text" value="" optional="true" label="Reference genome" help="Name of the reference genome in the MAF file (first found if empty)">
+            <expand macro="sanitizer_default"/>
+            <expand macro="validator_trim"/>
+        </param> 
+        <expand macro="params_targetGenomes_optional"/>
+        <conditional name="mode">
+            <param name="append" type="select" label="Output options">
+                <option value="false" selected="true">Create a new HAL file (default)</option>
+                <option value="true">Append MAF as subtree to an existing HAL file (--append)</option>
+            </param>
+            <when value="false">
+                <expand macro="hal_backend_format"/>   
+            </when>
+            <when value="true">
+                <expand macro="input_hal"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="hal" label="${tool.name} on ${on_string}: HAL file" from_work_dir="writable_hal.hal"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_maf" value="maf2halTest.maf"/>
+            <output name="output_file" ftype="hal">
+                <assert_contents>
+                    <has_size min="50000"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="Total Number of blocks in maf: 6"/>
+            </assert_stdout>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_maf" value="maf2halTest.maf.gz"/>
+            <output name="output_file" ftype="hal">
+                <assert_contents>
+                    <has_size min="50000"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="Total Number of blocks in maf: 6"/>
+            </assert_stdout>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_maf" value="maf2halTest.maf.bz2"/>
+            <output name="output_file" ftype="hal">
+                <assert_contents>
+                    <has_size min="50000"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="Total Number of blocks in maf: 6"/>
+            </assert_stdout>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_maf" value="maf2halTestAppend.maf"/>
+            <conditional name="mode">
+                <param name="append" value="true"/>
+                <param name="input_hal" value="maf2halTestAppend.hal"/>
+            </conditional>
+            <output name="output_file" ftype="hal">
+                <assert_contents>
+                    <has_size min="70000"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="Total Number of blocks in maf: 1"/>
+            </assert_stdout>
+        </test>
+        <!-- 
+        Disabled until mmap HAL format is allowed
+        <test expect_num_outputs="1">
+            <param name="input_maf" value="maf2halTest.maf"/>
+            <conditional name="mode">
+                <param name="append" value="false"/>
+                <conditional name="inputFormat">
+                    <param name="type" value="mmap"/>
+                    <param name="mmapFileSize" value="1"/>
+                </conditional>
+            </conditional>
+            <assert_stdout>
+                <has_text text="Total Number of blocks in maf: 6"/>
+            </assert_stdout>
+        </test>
+        -->
+    </tests>
+    <help><![CDATA[
+maf2hal takes a MAF alignment as input and produces a HAL database as output.
+It can build a new HAL file or attach the MAF as a subtree if the reference genome already exists as a leaf. 
+You can specify the reference genome and limit import to selected target genomes. 
+
+-----
+
+.. class:: warningmark
+
+Creating or importing a HAL file in mmap format can result in a corrupted HAL file. Run halValidate on the output HAL file before further analysis.
+
+.. class:: warningmark
+
+At the moment, creating a HAL file in mmap format is disabled. The creation in HDF5 format is enforced.
+    ]]></help>
+    <expand macro="citation"/>
+    <expand macro="creator"/>
+</tool>
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