# HG changeset patch
# User iuc
# Date 1659988130 0
# Node ID 3c3373dd1de4a540918d73c36f4e976b7b21457a
# Parent  21ffcb56d11190af663e4349a31430a0b42a00e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8

diff -r 21ffcb56d111 -r 3c3373dd1de4 macros.xml
--- a/macros.xml	Fri Jul 29 20:17:59 2022 +0000
+++ b/macros.xml	Mon Aug 08 19:48:50 2022 +0000
@@ -119,7 +119,7 @@
             <filter>'alignment_file' in extra_outputs</filter>
         </data>-->
         <data name="marker_gene_stats" format="tabular" from_work_dir="output/storage/marker_gene_stats.tsv"  label="${tool.name} on ${on_string}: Marker gene statistics">
-            <filter>'marker_gene_stats' in extra_outputs</filter>
+            <filter>extra_outputs and 'marker_gene_stats' in extra_outputs</filter>
         </data>
     </xml>
     <xml name="rank_taxon">
diff -r 21ffcb56d111 -r 3c3373dd1de4 tree.xml
--- a/tree.xml	Fri Jul 29 20:17:59 2022 +0000
+++ b/tree.xml	Mon Aug 08 19:48:50 2022 +0000
@@ -38,22 +38,22 @@
         <data name="concatenated_fasta" format="fasta" from_work_dir="output/storage/tree/concatenated.fasta" label="${tool.name} on ${on_string}: Concatenated masked sequences"/>
         <data name="concatenated_tre" format="phyloxml" from_work_dir="output/storage/tree/concatenated.tre" label="${tool.name} on ${on_string}: Concatenated tree"/>
         <collection name="hmmer_tree_ali" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMMER alignment file for each bin">
-            <filter>ali and 'hmmer_tree_ali' in extra_outputs</filter>
+            <filter>ali and extra_outputs and 'hmmer_tree_ali' in extra_outputs</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
         </collection>
         <data name="concatenated_pplacer_json" format="json" from_work_dir="output/storage/tree/concatenated.pplacer.json" label="${tool.name} on ${on_string}: Concatenated pplacer JSON">
-            <filter>'concatenate_pplacer_json' in extra_outputs</filter>
+            <filter>extra_outputs and 'concatenate_pplacer_json' in extra_outputs</filter>
         </data>
         <collection name="genes_fna" type="list" label="${tool.name} on ${on_string}: Protein gene sequences for each bin">
-            <filter>not genes and nt and 'genes_fna' in extra_outputs</filter>
+            <filter>not genes and nt and extra_outputs and 'genes_fna' in extra_outputs</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.fna" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/>
         </collection>
         <collection name="genes_faa" type="list" label="${tool.name} on ${on_string}: Nucleotide gene sequences for each bin">
-            <filter>'genes_faa' in extra_outputs</filter>
+            <filter>extra_outputs and 'genes_faa' in extra_outputs</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.faa" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/>
         </collection>
         <collection name="genes_gff" type="list" label="${tool.name} on ${on_string}: Gene feature files for each bin">
-            <filter>not genes and 'genes_gff' in extra_outputs</filter>
+            <filter>not genes and extra_outputs and 'genes_gff' in extra_outputs</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.gff" format="gff" directory="output/bins/" recurse="true" match_relative_path="true"/>
         </collection>
     </outputs>