--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/daa_meganizer.xml	Fri Dec 03 23:10:15 2021 +0000
@@ -0,0 +1,88 @@
+<tool id="megan_daa_meganizer" name="MEGAN: meganize a DIAMOND file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>for use with MEGAN</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+## daa-meganizer "meganizes" the input, altering
+## the file itself instead of producing a separate
+## output.  We'll make a copy of the input to handle
+## this issue.  The input must also have a .daa file
+## extension.
+#set input_identifier = 'input.' + $in.ext
+cp '${in}' '${input_identifier}' &&
+
+daa-meganizer
+--in '${input_identifier}'
+#if $advanced_options.metaDataFile:
+    --metaDataFile '$advanced_options.metaDataFile'
+#end if
+$advanced_options.longReads
+$advanced_options.classify
+--minScore $advanced_options.minScore
+--maxExpected $advanced_options.maxExpected
+--minPercentIdentity $advanced_options.minPercentIdentity
+--topPercent $advanced_options.topPercent
+--minSupportPercent $advanced_options.minSupportPercent
+--minSupport $advanced_options.minSupport
+--minPercentReadCover $advanced_options.minPercentReadCover
+--minPercentReferenceCover $advanced_options.minPercentReferenceCover
+--minReadLength $advanced_options.minReadLength
+--lcaAlgorithm '$advanced_options.lcaAlgorithm'
+--lcaCoveragePercent $advanced_options.lcaCoveragePercent
+--readAssignmentMode '$advanced_options.readAssignmentMode'
+#if $advanced_options.conFile:
+    --conFile '$advanced_options.conFile'
+#end if
+#if $advanced_options.mapDB:
+    --mapDB '$advanced_options.mapDB'
+#end if
+#if str($advanced_options.only) != '':
+    --only '$advanced_options.only'
+#end if
+--threads \${GALAXY_SLOTS:-8}
+--tempStoreDir '.'
+&& mv '$input_identifier' '$output'
+    ]]></command>
+    <inputs>
+        <param argument="--in" type="data" format="daa" label="Input DAA file"/>
+        <section name="advanced_options" title="Advanced options" expanded="false">
+            <param argument="--metaDataFile" type="data" format="tabular" multiple="true" optional="true" label="Files containing metadata to be included in the output files"/>
+            <expand macro="long_reads_param"/>
+            <expand macro="classify_param"/>
+            <expand macro="blast_params"/>
+            <expand macro="min_max_params"/>
+            <expand macro="lca_params"/>
+            <expand macro="read_assignment_mode_param"/>
+            <expand macro="con_file_param"/>
+            <expand macro="mapdb_param"/>
+            <param argument="--only" type="text" value="" label="Names of classifications to use" help="Leave blank to use all classifications">
+                <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output" format="daa"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in" ftype="daa" value="input.daa"/>
+            <output name="output" ftype="daa">
+                <assert_contents>
+                    <has_size value="3500"/>
+                </assert_contents>
+            </output>
+       </test>
+    </tests>
+    <help>
+**What it does**
+
+Meganizes a DIAMOND (i.e., a Direct Access Archive or DAA) file, a proprietary file format developed by PowerISO Computing
+for disk image files.  The output is a DIAMOND file consisting of the original input file, but with additional blocks of
+information appended to the end of the file.
+
+    </help>
+    <expand macro="citations"/>
+</tool>