# HG changeset patch
# User iuc
# Date 1659988888 0
# Node ID 2e995a9aa00edc999ecfdb7327ea63509f2cc3b0
# Parent  91230b9141c1164aa9fe3ffedcfbf5e36ad42c3c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8

diff -r 91230b9141c1 -r 2e995a9aa00e macros.xml
--- a/macros.xml	Fri Jul 29 20:32:07 2022 +0000
+++ b/macros.xml	Mon Aug 08 20:01:28 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 ${on_string}: Marker gene statistics">
-            <filter>'marker_gene_stats' in extra_outputs</filter>
+            <filter>extra_outputs and 'marker_gene_stats' in extra_outputs</filter>
         </data>
     </xml>
     <xml name="rank_taxon">
diff -r 91230b9141c1 -r 2e995a9aa00e taxonomy_wf.xml
--- a/taxonomy_wf.xml	Fri Jul 29 20:32:07 2022 +0000
+++ b/taxonomy_wf.xml	Mon Aug 08 20:01:28 2022 +0000
@@ -54,30 +54,30 @@
         <data name="results" format="tabular" label="${tool.name} on ${on_string}: Bin statistics"/>
         <!-- taxon_set outputs -->
         <data name="marker_file" format="tabular" from_work_dir="output/*.ms" label="${tool.name} on ${on_string}: Marker genes">
-            <filter>'marker_file' in extra_outputs</filter>
+            <filter>extra_outputs and 'marker_file' in extra_outputs</filter>
         </data>
         <!--analyze outputs-->
         <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin">
-            <filter>'hmmer_analyze' in extra_outputs</filter>
+            <filter>extra_outputs and 'hmmer_analyze' in extra_outputs</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
         </collection>
         <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats">
-            <filter>'bin_stats_analyze' in extra_outputs</filter>
+            <filter>extra_outputs and 'bin_stats_analyze' in extra_outputs</filter>
         </data>
         <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" >
-            <filter>'checkm_hmm_info' in extra_outputs</filter>
+            <filter>extra_outputs and 'checkm_hmm_info' in extra_outputs</filter>
         </data>
         <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin">
-            <filter>analyze['ali'] and 'hmmer_analyze_ali' in extra_outputs</filter>
+            <filter>analyze['ali'] and extra_outputs and 'hmmer_analyze_ali' in extra_outputs</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
         </collection>
         <!--qa outputs-->
         <data name="bin_stats_ext" format="tabular" from_work_dir="output/storage/bin_stats_ext.tsv" label="${tool.name} on ${on_string}: Marker gene bin extensive stats">
-            <filter>'bin_stats_ext' in extra_outputs</filter>
+            <filter>extra_outputs and 'bin_stats_ext' in extra_outputs</filter>
         </data>
         <expand macro="qa_extra_outputs" />
         <data name="marker_gene_stats" format="tabular" from_work_dir="output/storage/marker_gene_stats.tsv"  label="${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>
     </outputs>
     <tests>