Mercurial > repos > ebi-gxa > ct_get_tool_perf_table

comparison ct_get_tool_perf_table.xml @ 6:90d7f30478ee draft default tip

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:38:50 +0000
parents 424f8251a202
children
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5:424f8251a202 6:90d7f30478ee
1 <tool id="ct_get_tool_perf_table" name="Cell types - get tool performance table" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> 1 <tool id="ct_get_tool_perf_table" name="Cell types - get tool performance table" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>Get performance table for a list of outputs generated by various tools</description> 2 <description>Get performance table for a list of outputs generated by various tools</description>
3 <macros> 3 <macros>
4 <import>ct_macros.xml</import> 4 <import>ct_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
8 mkdir -p input_dir; 8 mkdir -p input_dir;
9 #for $input_file in $input_files: 9 #for $input_file in $input_files:
10 cp '$input_file' input_dir/; 10 cp '$input_file' input_dir/;
11 #end for 11 #end for
12 12
13 get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --num-cores \${GALAXY_SLOTS:-1} --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}" 13 get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}" --tmpdir ./
14 14
15 #if $exclusions 15 #if $exclusions
16 --exclusions "${exclusions}" 16 --exclusions "${exclusions}"
17 #end if 17 #end if
18 #if $ontology_graph 18 #if $ontology_graph
19 --ontology-graph "${ontology_graph}" 19 --ontology-graph "${ontology_graph}"
20 #end if
21 #if $parallel
22 --parallel "${parallel}"
23 #end if
24 #if $tmpdir
25 --tmpdir "${tmpdir}"
26 #end if 20 #end if
27 #if $include_sem_siml 21 #if $include_sem_siml
28 --include-sem-siml "${include_sem_siml}" 22 --include-sem-siml "${include_sem_siml}"
29 #end if 23 #end if
30 #if $barcode_col_ref 24 #if $barcode_col_ref
45 39
46 ]]></command> 40 ]]></command>
47 <inputs> 41 <inputs>
48 <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" /> 42 <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" />
49 <param type="data" name="ref_file" label="Reference metadata file" format="txt" help="Metadata file with reference labels" /> 43 <param type="data" name="ref_file" label="Reference metadata file" format="txt" help="Metadata file with reference labels" />
50 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
51 <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" /> 44 <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" />
52 <param type="data" name="exclusions" label="Exclusions" format="yml" optional="true" help="Config file with exclusions" /> 45 <param type="data" name="exclusions" label="Exclusions" format="yml" optional="true" help="Config file with exclusions" />
53 <param type="data" name="ontology_graph" label="Ontology graph" optional="true" format="obo" help="Ontology graph to run semantis similarity computations" /> 46 <param type="text" name="ontology_graph" label="Ontology graph" optional="true" help="Ontology graph to run semantis similarity computations" />
54 <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
55 <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" /> 47 <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />
56 <param type="text" name="barcode_col_ref" label="Reference file barcode field" value='cell_id' help="Name of barcode field in reference metadata file" /> 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">
57 <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file" /> 49 <expand macro="sanitize_strings" />
58 <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" /> 50 </param>
59 <param type="text" name="label_col_pred" label="Predicted file label column" value="predicted_label" help="Name of label field in predictions file" /> 51 <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file">
52 <expand macro="sanitize_strings" />
53 </param>
54 <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file">
55 <expand macro="sanitize_strings" />
56 </param>
57 <param type="text" name="label_col_pred" label="Predicted file label column" value="predicted_label" help="Name of label field in predictions file">
58 <expand macro="sanitize_strings" />
59 </param>
60 <expand macro="sem_siml_options" /> 60 <expand macro="sem_siml_options" />
61 </inputs> 61 </inputs>
62 <outputs> 62 <outputs>
63 <data name="output_path" format="txt" /> 63 <data name="output_path" format="txt" />
64 </outputs> 64 </outputs>
65 <tests> 65 <tests>
66 <test> 66 <test>
67 <param name="input_files" value="results_dir/garnett_output.txt,results_dir/scmap-cell_output.txt,results_dir/scmap-cluster_output.txt,results_dir/scpred_output.txt" /> 67 <param name="input_files" value="results_dir/garnett_output.txt,results_dir/scmap-cell_output.txt,results_dir/scmap-cluster_output.txt,results_dir/scpred_output.txt" />
68 <param name="ref_file" value="reference_sdrf.tsv" /> 68 <param name="ref_file" value="reference_sdrf.tsv" />
69 <param name="ontology_graph" value="cl-basic.obo" />
70 <param name="lab_cl_mapping" value="label_cl_dict.rds" /> 69 <param name="lab_cl_mapping" value="label_cl_dict.rds" />
71 <param name="parallel" value="TRUE" />
72 <param name="exclusions" value="exclusions.yml" /> 70 <param name="exclusions" value="exclusions.yml" />
73 <param name="barcode_col_ref" value="Assay" /> 71 <param name="barcode_col_ref" value="Assay" />
74 <param name="barcode_col_pred" value="cell_id" /> 72 <param name="barcode_col_pred" value="cell_id" />
75 <param name="label_col_ref" value="Sample.Characteristic.cell.type." /> 73 <param name="label_col_ref" value="Sample Characteristic[cell type]" />
76 <param name="label_col_pred" value="predicted_label" /> 74 <param name="label_col_pred" value="predicted_label" />
77 <output name="output_path" file="tool_perf_table.tsv" compare="sim_size" /> 75 <output name="output_path" file="tool_perf_table.tsv" compare="sim_size" />
78 </test> 76 </test>
79 </tests> 77 </tests>
80 <help><![CDATA[ 78 <help><![CDATA[