diff kaiju-mergeOutputs.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/kaiju-mergeOutputs.xml	Tue Apr 22 14:03:00 2025 +0000
@@ -0,0 +1,66 @@
+<tool id="kaiju_mergeoutputs" name="kaiju-mergeOutputs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        sort -k2,2 '$kaiju_table'  > kaiju.out.sort &&
+        sort -k2,2 '$kraken_table' > kraken.out.sort &&
+        kaiju-mergeOutputs
+            -i kaiju.out.sort
+            -j kraken.out.sort
+            -o '$combined_out'
+            -c $optional.conflict.mode
+            #if $optional.conflict.mode in ["lca", "lowest"]
+                -t '$reference.fields.path'/nodes.dmp
+            #end if
+            $optional.s
+            -v
+    ]]></command>
+    <inputs>
+        <param name="kaiju_table" type="data" format="tabular" label="kaiju output table"/>
+        <param name="kraken_table" type="data" format="tabular" label="Another output table" help="e.g. from kraken"/>
+        <section name="optional" title="Optional arguments" expanded="false">
+            <conditional name="conflict">
+                <param argument="-c" name="mode" type="select" label="Conflict resolution mode">
+                    <option value="1">use taxid from 1st input</option>
+                    <option value="2">use taxid from 2nd input</option>
+                    <option value="lca" selected="true">least common ancestor (LCA) of the two taxon IDs</option>
+                    <option value="lowest">lower rank of the two taxa is used if they are within the same lineage and LCA otherwise</option>
+                </param>
+                <when value="1"/>
+                <when value="2"/>
+                <when value="lca">
+                    <expand macro="reference"/>
+                </when>
+                <when value="lowest">
+                    <expand macro="reference"/>
+                </when>
+            </conditional>
+            <param argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Use score" help="Use 4th column with classification score to give precedence to taxon with better score" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="combined_out" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="kaiju_table" value="kaiju.out"/>
+            <param name="kraken_table" value="kaiju.out"/>
+            <output name="combined_out" value="kaiju.out"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+Merge two tab-separated output files in the column format (see above) used by Kaiju and Kraken. Only the first three columns are used.
+
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file