Mercurial > repos > iuc > checkm_lineage_wf

comparison lineage_wf.xml @ 1:f0107b9f2dc3 draft default tip

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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
comparison
equal deleted inserted replaced
0:760dc0c0e689 1:f0107b9f2dc3
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 ${on_string}: Phylogenetic HMM hits to each bin">
75 <filter>'hmmer_tree' in extra_outputs</filter> 75 <filter>extra_outputs and 'hmmer_tree' in extra_outputs</filter>
76 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> 76 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
77 </collection> 77 </collection>
78 <data name="concatenated_fasta" format="fasta" from_work_dir="output/storage/tree/concatenated.fasta" label="${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 ${on_string}: Phylogenetic HMMER alignment file for each bin">
85 <filter>tree_analyze['ali'] and 'hmmer_tree_ali' in extra_outputs</filter> 85 <filter>tree_analyze['ali'] and extra_outputs and 'hmmer_tree_ali' in extra_outputs</filter>
86 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> 86 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
87 </collection> 87 </collection>
88 <data name="concatenated_pplacer_json" format="json" from_work_dir="output/storage/tree/concatenated.pplacer.json" label="${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 ${on_string}: Protein gene sequences for each bin">
92 <filter>not tree_analyze['genes'] and tree_analyze['nt'] and 'genes_fna' in extra_outputs</filter> 92 <filter>not tree_analyze['genes'] and tree_analyze['nt'] and extra_outputs and 'genes_fna' in extra_outputs</filter>
93 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.fna" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/> 93 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.fna" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/>
94 </collection> 94 </collection>
95 <collection name="genes_faa" type="list" label="${tool.name} on ${on_string}: Nucleotide gene sequences for each bin"> 95 <collection name="genes_faa" type="list" label="${tool.name} on ${on_string}: Nucleotide gene sequences for each bin">
96 <filter>'genes_faa' in extra_outputs</filter> 96 <filter>extra_outputs and 'genes_faa' in extra_outputs</filter>
97 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.faa" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/> 97 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.faa" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/>
98 </collection> 98 </collection>
99 <collection name="genes_gff" type="list" label="${tool.name} on ${on_string}: Gene feature files for each bin"> 99 <collection name="genes_gff" type="list" label="${tool.name} on ${on_string}: Gene feature files for each bin">
100 <filter>not tree_analyze['genes'] and 'genes_gff' in extra_outputs</filter> 100 <filter>not tree_analyze['genes'] and extra_outputs and 'genes_gff' in extra_outputs</filter>
101 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.gff" format="gff" directory="output/bins/" recurse="true" match_relative_path="true"/> 101 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.gff" format="gff" directory="output/bins/" recurse="true" match_relative_path="true"/>
102 </collection> 102 </collection>
103 <!--lineage_set outputs--> 103 <!--lineage_set outputs-->
104 <data name="marker_file" format="tabular" from_work_dir="output/lineage.ms" label="${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 ${on_string}: Marker gene HMM hits to each bin">
109 <filter>'hmmer_analyze' in extra_outputs</filter> 109 <filter>extra_outputs and 'hmmer_analyze' in extra_outputs</filter>
110 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> 110 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
111 </collection> 111 </collection>
112 <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${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 ${on_string}: HMMER alignment file for each bin">
119 <filter>tree_analyze['ali'] and 'hmmer_analyze_ali' in extra_outputs</filter> 119 <filter>tree_analyze['ali'] and extra_outputs and 'hmmer_analyze_ali' in extra_outputs</filter>
120 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> 120 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
121 </collection> 121 </collection>
122 <!--qa outputs--> 122 <!--qa outputs-->
123 <data name="bin_stats_ext" format="tabular" from_work_dir="output/storage/bin_stats_ext.tsv" label="${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"/>