Mercurial > repos > ebi-gxa > ct_get_tool_perf_table
comparison ct_get_tool_perf_table.xml @ 4:d15f7509077b draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
author | ebi-gxa |
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date | Wed, 17 Jun 2020 12:31:30 -0400 |
parents | 71c809e81f66 |
children | 424f8251a202 |
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3:71c809e81f66 | 4:d15f7509077b |
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18 --exclusions "${exclusions}" | 18 --exclusions "${exclusions}" |
19 #end if | 19 #end if |
20 #if $parallel | 20 #if $parallel |
21 --parallel "${parallel}" | 21 --parallel "${parallel}" |
22 #end if | 22 #end if |
23 #if $include_sem_siml | |
24 --include-sem-siml "${include_sem_siml}" | |
25 #end if | |
23 #if $barcode_col_ref | 26 #if $barcode_col_ref |
24 --barcode-col-ref "${barcode_col_ref}" | 27 --barcode-col-ref "${barcode_col_ref}" |
25 #end if | 28 #end if |
26 #if $barcode_col_pred | 29 #if $barcode_col_pred |
27 --barcode-col-pred "${barcode_col_pred}" | 30 --barcode-col-pred "${barcode_col_pred}" |
34 #end if | 37 #end if |
35 #if $semantic_sim_metric | 38 #if $semantic_sim_metric |
36 --semantic-sim-metric "${semantic_sim_metric}" | 39 --semantic-sim-metric "${semantic_sim_metric}" |
37 #end if | 40 #end if |
38 | 41 |
39 | |
40 ]]></command> | 42 ]]></command> |
41 <inputs> | 43 <inputs> |
42 <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" /> | 44 <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" /> |
43 <param type="data" name="ref_file" label="Reference metadata file" format="txt" help="Metadata file with reference labels" /> | 45 <param type="data" name="ref_file" label="Reference metadata file" format="txt" help="Metadata file with reference labels" /> |
44 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" /> | 46 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" /> |
47 <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" /> | |
45 <param type="data" name="exclusions" label="Exclusions" format="yml" optional="true" help="Config file with exclusions" /> | 48 <param type="data" name="exclusions" label="Exclusions" format="yml" optional="true" help="Config file with exclusions" /> |
46 <param type="data" name="ontology_graph" label="Ontology graph" format="obo" help="Ontology graph to run semantis similarity computations" /> | 49 <param type="data" name="ontology_graph" label="Ontology graph" optional="true" format="obo" help="Ontology graph to run semantis similarity computations" /> |
50 <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" /> | |
47 <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" /> | 51 <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" /> |
48 <param type="text" name="barcode_col_ref" label="Reference file barcode field" value='cell_id' help="Name of barcode field in reference metadata file" /> | 52 <param type="text" name="barcode_col_ref" label="Reference file barcode field" value='cell_id' help="Name of barcode field in reference metadata file" /> |
49 <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file" /> | 53 <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file" /> |
50 <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" /> | 54 <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" /> |
51 <param type="text" name="label_col_pred" label="Predicted file label column" value="pred_label" help="Name of label field in predictions file" /> | 55 <param type="text" name="label_col_pred" label="Predicted file label column" value="pred_label" help="Name of label field in predictions file" /> |
52 <param type="text" name="semantic_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" /> | 56 <expand macro="sem_siml_options" /> |
53 </inputs> | 57 </inputs> |
54 <outputs> | 58 <outputs> |
55 <data name="output_path" format="txt" /> | 59 <data name="output_path" format="txt" /> |
56 </outputs> | 60 </outputs> |
57 <tests> | 61 <tests> |