diff macros.xml @ 0:cdc8a98ed4fc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju commit 59064c06143fdc7d7b17178e46911ba1009cd32e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Apr 22 14:03:00 2025 +0000
@@ -0,0 +1,96 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.10.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.2</token>
+
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">kaiju</xref>
+        </xrefs>
+    </xml>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">kaiju</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/ncomms11257</citation>
+        </citations>
+    </xml>
+
+    <xml name="reference">
+        <param name="reference" type="select" label="kaiju refernce data">
+            <options from_data_table="kaiju"/>
+            <validator type="no_options" message="No reference data installed. Ask your Galaxy admin."/>
+        </param>
+    </xml>
+
+    <xml name="r" tokens="optional">
+        <param argument="-r" name="rank" type="select" optional="@OPTIONAL@" label="rank">
+            <option value="phylum">phylum</option>
+            <option value="class">class</option>
+            <option value="order">order</option>
+            <option value="family">family</option>
+            <option value="genus">genus</option>
+            <option value="species">species</option>
+        </param>
+    </xml>
+
+    <xml name="l">
+        <param argument="-l" type="select" multiple="true" optional="true" label="Print taxon path containing selected ranks ranks specified ">
+            <option value="domain">Domain</option>
+            <option value="realm">Realm</option>
+            <option value="kingdom">Kingdom</option>
+            <option value="subkingdom">Subkingdom</option>
+            <option value="superphylum">Superphylum</option>
+            <option value="phylum">Phylum</option>
+            <option value="subphylum">Subphylum</option>
+            <option value="infraphylum">Infraphylum</option>
+            <option value="superclass">Superclass</option>
+            <option value="class">Class</option>
+            <option value="subclass">Subclass</option>
+            <option value="infraclass">Infraclass</option>
+            <option value="cohort">Cohort</option>
+            <option value="subcohort">Subcohort</option>
+            <option value="superorder">Superorder</option>
+            <option value="order">Order</option>
+            <option value="suborder">Suborder</option>
+            <option value="infraorder">Infraorder</option>
+            <option value="parvorder">Parvorder</option>
+            <option value="superfamily">Superfamily</option>
+            <option value="family">Family</option>
+            <option value="subfamily">Subfamily</option>
+            <option value="tribe">Tribe</option>
+            <option value="subtribe">Subtribe</option>
+            <option value="genus">Genus</option>
+            <option value="subgenus">Subgenus</option>
+            <option value="species_group">Species Group</option>
+            <option value="species_subgroup">Species Subgroup</option>
+            <option value="species">Species</option>
+            <option value="subspecies">Subspecies</option>
+            <option value="forma_specialis">Forma Specialis</option>
+            <option value="varietas">Variety</option>
+            <option value="subvariety">Subvariety</option>
+            <option value="forma">Form</option>
+            <option value="section">Section</option>
+            <option value="subsection">Subsection</option>
+            <option value="series">Series</option>
+            <option value="subseries">Subseries</option>
+            <option value="strain">Strain</option>
+            <option value="isolate">Isolate</option>
+            <option value="serogroup">Serogroup</option>
+            <option value="serotype">Serotype</option>
+            <option value="biotype">Biotype</option>
+            <option value="genotype">Genotype</option>
+            <option value="morph">Morph</option>
+            <option value="pathogroup">Pathogroup</option>
+        </param>
+    </xml>
+
+    <xml name="u">
+        <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Do not count unclassified reads" help="Disables counting unclassified reads towards the total number of reads when calculating percentages."/>
+    </xml>
+</macros>
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