diff macros.xml @ 1:2f8d3924bb3b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"

--- a/macros.xml	Wed Nov 24 21:52:14 2021 +0000
+++ b/macros.xml	Fri Dec 03 23:09:53 2021 +0000
@@ -38,6 +38,18 @@
             </when>
         </conditional>
     </macro>
+    <macro name="long_reads_param">
+        <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/>
+    </macro>
+    <macro name="classification_options">
+        <option value="EC" selected="true">EC</option>
+        <option value="EGGNOG">EGGNOG</option>
+        <option value="GTDB">GTDB</option>
+        <option value="INTERPRO2GO">INTERPRO2GO</option>
+        <option value="KEGG">KEGG</option>
+        <option value="SEED">SEED</option>
+        <option value="Taxonomy">Taxonomy</option>
+    </macro>
     <macro name="blast_mode_options">
         <option value="Unknown" selected="true">Unknown</option>
         <option value="BlastN">BlastN</option>
@@ -45,12 +57,42 @@
         <option value="BlastX">BlastX</option>
         <option value="Classifier">Classifier</option>
     </macro>
-    <macro name="common_blast_params">
+    <macro name="classify_param">
+        <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/>
+    </macro>
+    <macro name="blast_params">
         <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>
         <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/>
         <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/>
         <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/>
     </macro>
+    <macro name="min_max_params">
+        <param argument="--minSupportPercent" type="float" value="0.05" min="0.0" max="100.0" label="Minimum support as percent of assigned reads" help="0 value ignores"/>
+        <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/>
+        <param argument="--minPercentReadCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of read length to be covered by alignments"/>
+        <param argument="--minPercentReferenceCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of reference length to be covered by alignments"/>
+        <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/>
+    </macro>
+    <macro name="lca_params">
+        <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment">
+            <option value="naive" selected="true">naive</option>
+            <option value="weighted">weighted</option>
+            <option value="longReads">longReads</option>
+        </param>
+        <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/>
+    </macro>
+    <macro name="read_assignment_mode_param">
+        <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode">
+            <option value="alignedBases" selected="true">alignedBases</option>
+            <option value="readCount">readCount</option>
+        </param>
+    </macro>
+    <macro name="con_file_param">
+        <param argument="--conFile" type="data" format="txt" optional="true" label="File of contaminant taxa (one id or name per line)" help="Optional, no selection ignores"/>
+    </macro>
+    <macro name="mapdb_param">
+        <param argument="--mapDB" type="data" format="sqlite" optional="true" label="MEGAN mapping db" help="Optional, no selection ignores"/>
+    </macro>
     <xml name="sanitize_query" token_validinitial="string.printable">
         <sanitizer>
             <valid initial="@VALIDINITIAL@">
@@ -64,6 +106,8 @@
     </xml>
     <xml name="citations">
         <citations>
+            <citation type="doi">10.1038/nmeth.3176</citation>
+            <citation type="doi">10.1101/gr.120618.111</citation>
             <citation type="doi">10.1101/gr.5969107</citation>
         </citations>
     </xml>