Mercurial > repos > iuc > checkm_lineage_wf

changeset 1:f0107b9f2dc3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
author iuc
date Mon, 08 Aug 2022 19:59:56 +0000
parents 760dc0c0e689
children 8345d273ba82
files lineage_wf.xml macros.xml
diffstat 2 files changed, 17 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/lineage_wf.xml	Fri Jul 29 20:30:08 2022 +0000
+++ b/lineage_wf.xml	Mon Aug 08 19:59:56 2022 +0000
@@ -66,65 +66,64 @@
         <data name="results" format="tabular" label="${tool.name} on ${on_string}: Bin statistics"/>
         <!--tree outputs-->
         <data name="phylo_hmm_info" format="zip" from_work_dir="output/storage/phylo_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Phylogenetic HMM model info for each bin">
-            <filter>'phylo_hmm_info' in extra_outputs</filter>
+            <filter>extra_outputs and 'phylo_hmm_info' in extra_outputs</filter>
         </data>
         <data name="bin_stats_tree" format="tabular" from_work_dir="output/storage/bin_stats.tree.tsv" label="${tool.name} on ${on_string}: Phylogenetic bin stats">
-            <filter>'bin_stats_tree' in extra_outputs</filter>
+            <filter>extra_outputs and 'bin_stats_tree' in extra_outputs</filter>
         </data>
         <collection name="hmmer_tree" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMM hits to each bin">
-            <filter>'hmmer_tree' in extra_outputs</filter>
+            <filter>extra_outputs and 'hmmer_tree' in extra_outputs</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
         </collection>
         <data name="concatenated_fasta" format="fasta" from_work_dir="output/storage/tree/concatenated.fasta" label="${tool.name} on ${on_string}: Concatenated masked sequences">
-            <filter>'concatenated_fasta' in extra_outputs</filter>
+            <filter>extra_outputs and 'concatenated_fasta' in extra_outputs</filter>
         </data>
         <data name="concatenated_tre" format="phyloxml" from_work_dir="output/storage/tree/concatenated.tre" label="${tool.name} on ${on_string}: Concatenated tree">
-            <filter>'concatenated_tre' in extra_outputs</filter>
+            <filter>extra_outputs and 'concatenated_tre' in extra_outputs</filter>
         </data>
         <collection name="hmmer_tree_ali" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMMER alignment file for each bin">
-            <filter>tree_analyze['ali'] and 'hmmer_tree_ali' in extra_outputs</filter>
+            <filter>tree_analyze['ali'] and extra_outputs and 'hmmer_tree_ali' in extra_outputs</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
         </collection>
         <data name="concatenated_pplacer_json" format="json" from_work_dir="output/storage/tree/concatenated.pplacer.json" label="${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 ${on_string}: Protein gene sequences for each bin">
-            <filter>not tree_analyze['genes'] and tree_analyze['nt'] and 'genes_fna' in extra_outputs</filter>
+            <filter>not tree_analyze['genes'] and tree_analyze['nt'] and extra_outputs and 'genes_fna' in extra_outputs</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.fna" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/>
         </collection>
         <collection name="genes_faa" type="list" label="${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 ${on_string}: Gene feature files for each bin">
-            <filter>not tree_analyze['genes'] and 'genes_gff' in extra_outputs</filter>
+            <filter>not tree_analyze['genes'] and extra_outputs and 'genes_gff' in extra_outputs</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.gff" format="gff" directory="output/bins/" recurse="true" match_relative_path="true"/>
         </collection>
         <!--lineage_set outputs-->
         <data name="marker_file" format="tabular" from_work_dir="output/lineage.ms" label="${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 ${on_string}: HMMER alignment file for each bin">
-            <filter>tree_analyze['ali'] and 'hmmer_analyze_ali' in extra_outputs</filter>
+            <filter>tree_analyze['ali'] and extra_outputs and 'hmmer_analyze_ali' in extra_outputs</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
         </collection>
         <!--qa outputs-->
         <data name="bin_stats_ext" format="tabular" from_work_dir="output/storage/bin_stats_ext.tsv" label="${tool.name} on ${on_string}: Marker gene bin extensive stats">
-            <filter>'bin_stats_ext' in extra_outputs</filter>
+            <filter>extra_outputs and 'bin_stats_ext' in extra_outputs</filter>
         </data>
         <expand macro="qa_extra_outputs" />
-
     </outputs>
     <tests>
         <test expect_num_outputs="1">
--- a/macros.xml	Fri Jul 29 20:30:08 2022 +0000
+++ b/macros.xml	Mon Aug 08 19:59:56 2022 +0000
@@ -119,7 +119,7 @@
             <filter>'alignment_file' in extra_outputs</filter>
         </data>-->
         <data name="marker_gene_stats" format="tabular" from_work_dir="output/storage/marker_gene_stats.tsv"  label="${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">