Mercurial > repos > iuc > megan_blast2lca

diff blast2lca.xml @ 1:a5ed123d58d7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
author iuc
date Fri, 03 Dec 2021 23:08:32 +0000
parents 4187fcb0fd74
children 56deffcab3cc
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--- a/blast2lca.xml	Wed Nov 24 21:51:18 2021 +0000
+++ b/blast2lca.xml	Fri Dec 03 23:08:32 2021 +0000
@@ -76,11 +76,11 @@
             <param argument="--showRanks" type="boolean" truevalue="--showRanks" falsevalue="" checked="true" label="Show taxonomic ranks?"/>
             <param argument="--officialRanksOnly" type="boolean" truevalue="--officialRanksOnly" falsevalue="" checked="true" label="Report only taxa that have an official rank?"/>
             <param  argument="--showTaxIds" type="boolean" truevalue="--showTaxIds" falsevalue="" checked="false" label="Report taxon ids rather than taxon names?"/>
-            <expand macro="common_blast_params"/>
+            <expand macro="blast_params"/>
             <param argument="--maxKeggPerRead" type="integer" value="4" label="Maximum number of KEGG assignments to report for a read"/>
             <param argument="--applyTopPercentKegg" type="boolean" truevalue="--applyTopPercentKegg" falsevalue="" checked="true" label="Apply top percent filter in KEGG KO analysis?"/>
             <param argument="--parseTaxonNames" type="boolean" truevalue="--parseTaxonNames" falsevalue="" checked="true" label="Apply top percent filter in KEGG KO analysis?"/>
-            <param argument="--mapDB" type="data" format="sqlite" optional="true" label="MEGAN mapping db"/>
+            <expand macro="mapdb_param"/>
             <param argument="--acc2taxa" type="data" format="sqlite" optional="true" label="Accession-to-Taxonomy mapping file"/>
             <param argument="--syn2taxa" type="data" format="sqlite" optional="true" label="Synonyms-to-Taxonomy mapping file"/>
             <param argument="--acc2kegg" type="data" format="sqlite" optional="true" label="Accession-to-KEGG mapping file"/>
@@ -136,8 +136,6 @@
 To perform this analysis, MEGAN uses a mapping of GI numbers to KO groups. Hence, if a KEGG-based analysis is desired, then
 the database that is used in the BLAST alignment must contain GI numbers.
     </help>
-    <citations>
-        <citation type="doi">https://doi.org/10.1101/050559</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>