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comparison tree.xml @ 1:6d1c282e2ce2 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 19:59:26 +0000
parents 9b2790bca5b5
children
comparison
equal deleted inserted replaced
0:9b2790bca5b5 1:6d1c282e2ce2
36 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> 36 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
37 </collection> 37 </collection>
38 <data name="concatenated_fasta" format="fasta" from_work_dir="output/storage/tree/concatenated.fasta" label="${tool.name} on ${on_string}: Concatenated masked sequences"/> 38 <data name="concatenated_fasta" format="fasta" from_work_dir="output/storage/tree/concatenated.fasta" label="${tool.name} on ${on_string}: Concatenated masked sequences"/>
39 <data name="concatenated_tre" format="phyloxml" from_work_dir="output/storage/tree/concatenated.tre" label="${tool.name} on ${on_string}: Concatenated tree"/> 39 <data name="concatenated_tre" format="phyloxml" from_work_dir="output/storage/tree/concatenated.tre" label="${tool.name} on ${on_string}: Concatenated tree"/>
40 <collection name="hmmer_tree_ali" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMMER alignment file for each bin"> 40 <collection name="hmmer_tree_ali" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMMER alignment file for each bin">
41 <filter>ali and 'hmmer_tree_ali' in extra_outputs</filter> 41 <filter>ali and extra_outputs and 'hmmer_tree_ali' in extra_outputs</filter>
42 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> 42 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
43 </collection> 43 </collection>
44 <data name="concatenated_pplacer_json" format="json" from_work_dir="output/storage/tree/concatenated.pplacer.json" label="${tool.name} on ${on_string}: Concatenated pplacer JSON"> 44 <data name="concatenated_pplacer_json" format="json" from_work_dir="output/storage/tree/concatenated.pplacer.json" label="${tool.name} on ${on_string}: Concatenated pplacer JSON">
45 <filter>'concatenate_pplacer_json' in extra_outputs</filter> 45 <filter>extra_outputs and 'concatenate_pplacer_json' in extra_outputs</filter>
46 </data> 46 </data>
47 <collection name="genes_fna" type="list" label="${tool.name} on ${on_string}: Protein gene sequences for each bin"> 47 <collection name="genes_fna" type="list" label="${tool.name} on ${on_string}: Protein gene sequences for each bin">
48 <filter>not genes and nt and 'genes_fna' in extra_outputs</filter> 48 <filter>not genes and nt and extra_outputs and 'genes_fna' in extra_outputs</filter>
49 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.fna" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/> 49 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.fna" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/>
50 </collection> 50 </collection>
51 <collection name="genes_faa" type="list" label="${tool.name} on ${on_string}: Nucleotide gene sequences for each bin"> 51 <collection name="genes_faa" type="list" label="${tool.name} on ${on_string}: Nucleotide gene sequences for each bin">
52 <filter>'genes_faa' in extra_outputs</filter> 52 <filter>extra_outputs and 'genes_faa' in extra_outputs</filter>
53 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.faa" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/> 53 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.faa" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/>
54 </collection> 54 </collection>
55 <collection name="genes_gff" type="list" label="${tool.name} on ${on_string}: Gene feature files for each bin"> 55 <collection name="genes_gff" type="list" label="${tool.name} on ${on_string}: Gene feature files for each bin">
56 <filter>not genes and 'genes_gff' in extra_outputs</filter> 56 <filter>not genes and extra_outputs and 'genes_gff' in extra_outputs</filter>
57 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.gff" format="gff" directory="output/bins/" recurse="true" match_relative_path="true"/> 57 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.gff" format="gff" directory="output/bins/" recurse="true" match_relative_path="true"/>
58 </collection> 58 </collection>
59 </outputs> 59 </outputs>
60 <tests> 60 <tests>
61 <test expect_num_outputs="6"> 61 <test expect_num_outputs="6">