comparison ct_get_empirical_dist.xml @ 0:196cc72cebd1 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
author ebi-gxa
date Wed, 08 Apr 2020 11:34:54 -0400
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children 9d5e6a4ec5b5
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-1:000000000000 0:196cc72cebd1
1 <tool id="ct_get_empirical_dist" name="Cell types - get empirical distribution" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>Get empirical distribution for tool performance table</description>
3 <macros>
4 <import>ct_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8
9 ln -s $'${ontology_graph}' cl-basic.obo;
10
11 get_empirical_dist.R --input-ref-file "${input_ref_file}" --parallel "${parallel}" --exclusions "${exclusions}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}" --num-cores "${num_cores}" --ontology-graph cl-basic.obo --semantic-sim-metric "${sem_sim_metric}" --output-path "${output_list_path}" ]]></command>
12 <inputs>
13 <param type="data" name="input_ref_file" label="Input reference file" format="tsv" help="Text file with reference cell labels" />
14 <param type="data" name="exclusions" format="yml" label="Exclusions file" help="YML file with excluded/unlabelled terms" />
15 <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" />
16 <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />
17 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
18 <param type="integer" name="num_iter" value='5' label="Number of iterations" help="Number of simulations to generate empirical CDF" />
19 <param type="integer" name="num_cores" value='4' label="Number of cores" help="Number of cores to run the process" />
20 <param type="data" name="ontology_graph" label="Ontology graph" format="obo" help="Ontology graph to run semantis similarity computations" />
21 <param type="text" name="sem_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
22 </inputs>
23 <outputs>
24 <data name="output_list_path" format="rdata" />
25 </outputs>
26 <tests>
27 <test>
28 <param name="input_ref_file" value="reference_sdrf.tsv" />
29 <param name="label_col_ref" value="Sample.Characteristic.cell.type." />
30 <param name="ontology_graph" value="cl-basic.obo" />
31 <param name="exclusions" value="exclusions.yml" />
32 <param name="parallel" value="TRUE" />
33 <param name="lab_cl_mapping" value="label_cl_dict.rds" />
34 <output name="output_list_path" file="empirical_dist_list.rds" compare="sim_size" />
35 </test>
36 </tests>
37 <help><![CDATA[
38 @HELP@
39
40 @VERSION_HISTORY@
41 ]]></help>
42 <expand macro="citations" />
43 </tool>