Mercurial > repos > iuc > checkm_taxonomy_wf

comparison taxonomy_wf.xml @ 1:2e995a9aa00e 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 20:01:28 +0000
parents 91230b9141c1
children 19e4e2d98ebb
comparison
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0:91230b9141c1 1:2e995a9aa00e
52 </inputs> 52 </inputs>
53 <outputs> 53 <outputs>
54 <data name="results" format="tabular" label="${tool.name} on ${on_string}: Bin statistics"/> 54 <data name="results" format="tabular" label="${tool.name} on ${on_string}: Bin statistics"/>
55 <!-- taxon_set outputs --> 55 <!-- taxon_set outputs -->
56 <data name="marker_file" format="tabular" from_work_dir="output/*.ms" label="${tool.name} on ${on_string}: Marker genes"> 56 <data name="marker_file" format="tabular" from_work_dir="output/*.ms" label="${tool.name} on ${on_string}: Marker genes">
57 <filter>'marker_file' in extra_outputs</filter> 57 <filter>extra_outputs and 'marker_file' in extra_outputs</filter>
58 </data> 58 </data>
59 <!--analyze outputs--> 59 <!--analyze outputs-->
60 <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin"> 60 <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin">
61 <filter>'hmmer_analyze' in extra_outputs</filter> 61 <filter>extra_outputs and 'hmmer_analyze' in extra_outputs</filter>
62 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> 62 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
63 </collection> 63 </collection>
64 <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats"> 64 <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats">
65 <filter>'bin_stats_analyze' in extra_outputs</filter> 65 <filter>extra_outputs and 'bin_stats_analyze' in extra_outputs</filter>
66 </data> 66 </data>
67 <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" > 67 <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" >
68 <filter>'checkm_hmm_info' in extra_outputs</filter> 68 <filter>extra_outputs and 'checkm_hmm_info' in extra_outputs</filter>
69 </data> 69 </data>
70 <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin"> 70 <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin">
71 <filter>analyze['ali'] and 'hmmer_analyze_ali' in extra_outputs</filter> 71 <filter>analyze['ali'] and extra_outputs and 'hmmer_analyze_ali' in extra_outputs</filter>
72 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> 72 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
73 </collection> 73 </collection>
74 <!--qa outputs--> 74 <!--qa outputs-->
75 <data name="bin_stats_ext" format="tabular" from_work_dir="output/storage/bin_stats_ext.tsv" label="${tool.name} on ${on_string}: Marker gene bin extensive stats"> 75 <data name="bin_stats_ext" format="tabular" from_work_dir="output/storage/bin_stats_ext.tsv" label="${tool.name} on ${on_string}: Marker gene bin extensive stats">
76 <filter>'bin_stats_ext' in extra_outputs</filter> 76 <filter>extra_outputs and 'bin_stats_ext' in extra_outputs</filter>
77 </data> 77 </data>
78 <expand macro="qa_extra_outputs" /> 78 <expand macro="qa_extra_outputs" />
79 <data name="marker_gene_stats" format="tabular" from_work_dir="output/storage/marker_gene_stats.tsv" label="${tool.name} on ${on_string}: Marker gene statistics"> 79 <data name="marker_gene_stats" format="tabular" from_work_dir="output/storage/marker_gene_stats.tsv" label="${tool.name} on ${on_string}: Marker gene statistics">
80 <filter>'marker_gene_stats' in extra_outputs</filter> 80 <filter>extra_outputs and 'marker_gene_stats' in extra_outputs</filter>
81 </data> 81 </data>
82 </outputs> 82 </outputs>
83 <tests> 83 <tests>
84 <test expect_num_outputs="1"> 84 <test expect_num_outputs="1">
85 <conditional name="bins"> 85 <conditional name="bins">