Mercurial > repos > iuc > drep_dereplicate

changeset 11:f54e7b3da33c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 802d7fe606623d900fd0d5de157e87166c0b7e84
author iuc
date Wed, 07 May 2025 11:02:10 +0000
parents a0c4b280e67c
children
files macros.xml
diffstat 1 files changed, 25 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Apr 22 14:29:13 2025 +0000
+++ b/macros.xml	Wed May 07 11:02:10 2025 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">3.6.2</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="biotools">
         <xrefs>
@@ -336,6 +336,16 @@
             <option value="Secondary_clustering_dendrograms">Secondary_clustering_dendrograms.pdf</option>
             <option value="Secondary_clustering_MDS">Secondary_clustering_MDS.pdf</option>
             <option value="Clustering_scatterplots" selected="true">Clustering_scatterplots.pdf</option>
+            <option value="Bdb">Bdb.csv Basic genome statistics</option>
+            <option value="Cdb">Cdb.csv Clustering results</option>
+            <option value="Mdb">Mdb.csv Mash distance matrix</option>
+            <option value="Ndb">Ndb.csv ANI results between representative genomes</option>
+        <!-- Tdb
+            Taxonomy (as determined by centrifuge)
+        Sdb
+            The score of each genome
+        Wdb
+            The cluster and score of de-replicated genomes -->
             <yield/>
         </param>
     </xml>
@@ -343,8 +353,8 @@
         <expand macro="select_outputs">
             <option value="Cluster_scoring">Cluster_scoring.pdf</option>
             <option value="Winning_genomes">Winning_genomes.pdf</option>
-            <option value="Widb">Widb.csv</option>
-            <option value="Chdb">Chdb.tsv</option>
+            <option value="Widb">Widb.csv CheckM information on de-replicated genomes</option>
+            <option value="Chdb">Chdb.tsv CheckM results for all genomes</option>
         </expand>
     </xml>
     <xml name="test_default_select_drep_outputs">
@@ -373,6 +383,18 @@
         <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf">
             <filter>'Clustering_scatterplots' in select_outputs</filter>
         </data>
+        <data name="Bdb" format="csv" label="${tool.name} on ${on_string}: Bdb Basic genome statistics" from_work_dir="outdir/data_tables/Bdb.csv">
+            <filter>'' in select_outputs</filter>
+        </data>
+        <data name="Cdb" format="csv" label="${tool.name} on ${on_string}: Cdb Clustering results" from_work_dir="outdir/data_tables/Cdb.csv">
+            <filter>'Cdb' in select_outputs</filter>
+        </data>
+        <data name="Mdb" format="csv" label="${tool.name} on ${on_string}: Mdb Mash distance matrix" from_work_dir="outdir/data_tables/Mdb.csv">
+            <filter>'' in select_outputs</filter>
+        </data>
+        <data name="Ndb" format="csv" label="${tool.name} on ${on_string}: Ndb ANI results between representative genomes" from_work_dir="outdir/data_tables/Ndb.csv">
+            <filter>'Ndb' in select_outputs</filter>
+        </data>
     </xml>
     <xml name="drep_outputs">
         <expand macro="common_outputs"/>