Mercurial > repos > iuc > checkm_lineage_wf
comparison lineage_wf.xml @ 1:f0107b9f2dc3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
author | iuc |
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date | Mon, 08 Aug 2022 19:59:56 +0000 |
parents | 760dc0c0e689 |
children |
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0:760dc0c0e689 | 1:f0107b9f2dc3 |
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64 </inputs> | 64 </inputs> |
65 <outputs> | 65 <outputs> |
66 <data name="results" format="tabular" label="${tool.name} on ${on_string}: Bin statistics"/> | 66 <data name="results" format="tabular" label="${tool.name} on ${on_string}: Bin statistics"/> |
67 <!--tree outputs--> | 67 <!--tree outputs--> |
68 <data name="phylo_hmm_info" format="zip" from_work_dir="output/storage/phylo_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Phylogenetic HMM model info for each bin"> | 68 <data name="phylo_hmm_info" format="zip" from_work_dir="output/storage/phylo_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Phylogenetic HMM model info for each bin"> |
69 <filter>'phylo_hmm_info' in extra_outputs</filter> | 69 <filter>extra_outputs and 'phylo_hmm_info' in extra_outputs</filter> |
70 </data> | 70 </data> |
71 <data name="bin_stats_tree" format="tabular" from_work_dir="output/storage/bin_stats.tree.tsv" label="${tool.name} on ${on_string}: Phylogenetic bin stats"> | 71 <data name="bin_stats_tree" format="tabular" from_work_dir="output/storage/bin_stats.tree.tsv" label="${tool.name} on ${on_string}: Phylogenetic bin stats"> |
72 <filter>'bin_stats_tree' in extra_outputs</filter> | 72 <filter>extra_outputs and 'bin_stats_tree' in extra_outputs</filter> |
73 </data> | 73 </data> |
74 <collection name="hmmer_tree" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMM hits to each bin"> | 74 <collection name="hmmer_tree" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMM hits to each bin"> |
75 <filter>'hmmer_tree' in extra_outputs</filter> | 75 <filter>extra_outputs and 'hmmer_tree' in extra_outputs</filter> |
76 <discover_datasets pattern="(?P<designation>.*)/hmmer\.tree\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> | 76 <discover_datasets pattern="(?P<designation>.*)/hmmer\.tree\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> |
77 </collection> | 77 </collection> |
78 <data name="concatenated_fasta" format="fasta" from_work_dir="output/storage/tree/concatenated.fasta" label="${tool.name} on ${on_string}: Concatenated masked sequences"> | 78 <data name="concatenated_fasta" format="fasta" from_work_dir="output/storage/tree/concatenated.fasta" label="${tool.name} on ${on_string}: Concatenated masked sequences"> |
79 <filter>'concatenated_fasta' in extra_outputs</filter> | 79 <filter>extra_outputs and 'concatenated_fasta' in extra_outputs</filter> |
80 </data> | 80 </data> |
81 <data name="concatenated_tre" format="phyloxml" from_work_dir="output/storage/tree/concatenated.tre" label="${tool.name} on ${on_string}: Concatenated tree"> | 81 <data name="concatenated_tre" format="phyloxml" from_work_dir="output/storage/tree/concatenated.tre" label="${tool.name} on ${on_string}: Concatenated tree"> |
82 <filter>'concatenated_tre' in extra_outputs</filter> | 82 <filter>extra_outputs and 'concatenated_tre' in extra_outputs</filter> |
83 </data> | 83 </data> |
84 <collection name="hmmer_tree_ali" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMMER alignment file for each bin"> | 84 <collection name="hmmer_tree_ali" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMMER alignment file for each bin"> |
85 <filter>tree_analyze['ali'] and 'hmmer_tree_ali' in extra_outputs</filter> | 85 <filter>tree_analyze['ali'] and extra_outputs and 'hmmer_tree_ali' in extra_outputs</filter> |
86 <discover_datasets pattern="(?P<designation>.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> | 86 <discover_datasets pattern="(?P<designation>.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> |
87 </collection> | 87 </collection> |
88 <data name="concatenated_pplacer_json" format="json" from_work_dir="output/storage/tree/concatenated.pplacer.json" label="${tool.name} on ${on_string}: Concatenated pplacer JSON"> | 88 <data name="concatenated_pplacer_json" format="json" from_work_dir="output/storage/tree/concatenated.pplacer.json" label="${tool.name} on ${on_string}: Concatenated pplacer JSON"> |
89 <filter>'concatenate_pplacer_json' in extra_outputs</filter> | 89 <filter>extra_outputs and 'concatenate_pplacer_json' in extra_outputs</filter> |
90 </data> | 90 </data> |
91 <collection name="genes_fna" type="list" label="${tool.name} on ${on_string}: Protein gene sequences for each bin"> | 91 <collection name="genes_fna" type="list" label="${tool.name} on ${on_string}: Protein gene sequences for each bin"> |
92 <filter>not tree_analyze['genes'] and tree_analyze['nt'] and 'genes_fna' in extra_outputs</filter> | 92 <filter>not tree_analyze['genes'] and tree_analyze['nt'] and extra_outputs and 'genes_fna' in extra_outputs</filter> |
93 <discover_datasets pattern="(?P<designation>.*)/genes\.fna" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/> | 93 <discover_datasets pattern="(?P<designation>.*)/genes\.fna" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/> |
94 </collection> | 94 </collection> |
95 <collection name="genes_faa" type="list" label="${tool.name} on ${on_string}: Nucleotide gene sequences for each bin"> | 95 <collection name="genes_faa" type="list" label="${tool.name} on ${on_string}: Nucleotide gene sequences for each bin"> |
96 <filter>'genes_faa' in extra_outputs</filter> | 96 <filter>extra_outputs and 'genes_faa' in extra_outputs</filter> |
97 <discover_datasets pattern="(?P<designation>.*)/genes\.faa" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/> | 97 <discover_datasets pattern="(?P<designation>.*)/genes\.faa" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/> |
98 </collection> | 98 </collection> |
99 <collection name="genes_gff" type="list" label="${tool.name} on ${on_string}: Gene feature files for each bin"> | 99 <collection name="genes_gff" type="list" label="${tool.name} on ${on_string}: Gene feature files for each bin"> |
100 <filter>not tree_analyze['genes'] and 'genes_gff' in extra_outputs</filter> | 100 <filter>not tree_analyze['genes'] and extra_outputs and 'genes_gff' in extra_outputs</filter> |
101 <discover_datasets pattern="(?P<designation>.*)/genes\.gff" format="gff" directory="output/bins/" recurse="true" match_relative_path="true"/> | 101 <discover_datasets pattern="(?P<designation>.*)/genes\.gff" format="gff" directory="output/bins/" recurse="true" match_relative_path="true"/> |
102 </collection> | 102 </collection> |
103 <!--lineage_set outputs--> | 103 <!--lineage_set outputs--> |
104 <data name="marker_file" format="tabular" from_work_dir="output/lineage.ms" label="${tool.name} on ${on_string}: Marker genes"> | 104 <data name="marker_file" format="tabular" from_work_dir="output/lineage.ms" label="${tool.name} on ${on_string}: Marker genes"> |
105 <filter>'marker_file' in extra_outputs</filter> | 105 <filter>extra_outputs and 'marker_file' in extra_outputs</filter> |
106 </data> | 106 </data> |
107 <!--analyze outputs--> | 107 <!--analyze outputs--> |
108 <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin"> | 108 <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin"> |
109 <filter>'hmmer_analyze' in extra_outputs</filter> | 109 <filter>extra_outputs and 'hmmer_analyze' in extra_outputs</filter> |
110 <discover_datasets pattern="(?P<designation>.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> | 110 <discover_datasets pattern="(?P<designation>.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> |
111 </collection> | 111 </collection> |
112 <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats"> | 112 <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats"> |
113 <filter>'bin_stats_analyze' in extra_outputs</filter> | 113 <filter>extra_outputs and 'bin_stats_analyze' in extra_outputs</filter> |
114 </data> | 114 </data> |
115 <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" > | 115 <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" > |
116 <filter>'checkm_hmm_info' in extra_outputs</filter> | 116 <filter>extra_outputs and 'checkm_hmm_info' in extra_outputs</filter> |
117 </data> | 117 </data> |
118 <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin"> | 118 <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin"> |
119 <filter>tree_analyze['ali'] and 'hmmer_analyze_ali' in extra_outputs</filter> | 119 <filter>tree_analyze['ali'] and extra_outputs and 'hmmer_analyze_ali' in extra_outputs</filter> |
120 <discover_datasets pattern="(?P<designation>.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> | 120 <discover_datasets pattern="(?P<designation>.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> |
121 </collection> | 121 </collection> |
122 <!--qa outputs--> | 122 <!--qa outputs--> |
123 <data name="bin_stats_ext" format="tabular" from_work_dir="output/storage/bin_stats_ext.tsv" label="${tool.name} on ${on_string}: Marker gene bin extensive stats"> | 123 <data name="bin_stats_ext" format="tabular" from_work_dir="output/storage/bin_stats_ext.tsv" label="${tool.name} on ${on_string}: Marker gene bin extensive stats"> |
124 <filter>'bin_stats_ext' in extra_outputs</filter> | 124 <filter>extra_outputs and 'bin_stats_ext' in extra_outputs</filter> |
125 </data> | 125 </data> |
126 <expand macro="qa_extra_outputs" /> | 126 <expand macro="qa_extra_outputs" /> |
127 | |
128 </outputs> | 127 </outputs> |
129 <tests> | 128 <tests> |
130 <test expect_num_outputs="1"> | 129 <test expect_num_outputs="1"> |
131 <conditional name="bins"> | 130 <conditional name="bins"> |
132 <param name="select" value="individual"/> | 131 <param name="select" value="individual"/> |