Mercurial > repos > ebi-gxa > ct_get_empirical_dist
comparison ct_get_empirical_dist.xml @ 1:9d5e6a4ec5b5 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
author | ebi-gxa |
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date | Fri, 24 Apr 2020 11:20:00 -0400 |
parents | 196cc72cebd1 |
children | 25bb7e49e10d |
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0:196cc72cebd1 | 1:9d5e6a4ec5b5 |
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4 <import>ct_macros.xml</import> | 4 <import>ct_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 | 8 |
9 ln -s $'${ontology_graph}' cl-basic.obo; | 9 ln -s $'${ontology_graph}' cl-basic.obo; |
10 | 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 "${output_list_path}" ]]></command> | 11 get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}" --num-cores \${GALAXY_SLOTS:-1} --ontology-graph cl-basic.obo --output-path "${output_list_path}" |
12 | |
13 #if $parallel | |
14 --parallel "${parallel}" | |
15 #end if | |
16 #if $exclusions | |
17 --exclusions "${exclusions}" | |
18 #end if | |
19 #if $exclusions | |
20 --semantic-sim-metric "${sem_sim_metric}" | |
21 #end if | |
22 ]]></command> | |
12 <inputs> | 23 <inputs> |
13 <param type="data" name="input_ref_file" label="Input reference file" format="tsv" help="Text file with reference cell labels" /> | 24 <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" /> | 25 <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" /> | 26 <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" /> | 27 <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?" /> | 28 <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" /> | 29 <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" /> | 30 <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" /> | 31 <param type="text" name="sem_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" /> |
22 </inputs> | 32 </inputs> |
23 <outputs> | 33 <outputs> |
24 <data name="output_list_path" format="rdata" /> | 34 <data name="output_list_path" format="rdata" /> |