Mercurial > repos > ebi-gxa > ct_get_tool_perf_table

comparison ct_get_tool_perf_table.xml @ 4:d15f7509077b draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
author ebi-gxa
date Wed, 17 Jun 2020 12:31:30 -0400
parents 71c809e81f66
children 424f8251a202
comparison
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3:71c809e81f66 4:d15f7509077b
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>