comparison ct_get_empirical_dist.xml @ 4:5bf2827cd314 draft

"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 12:30:58 -0400
parents ce70358b0fe3
children 36eab91e0ff5
comparison
equal deleted inserted replaced
3:ce70358b0fe3 4:5bf2827cd314
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 "${output_list_path}" 11 get_empirical_dist.R --input-ref-file "${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 12
13 #if $parallel 13 #if $parallel
14 --parallel "${parallel}" 14 --parallel "${parallel}"
15 #end if 15 #end if
16 #if $sample_labs
17 --sample-labs "${sample_labs}"
18 #end if
16 #if $exclusions 19 #if $exclusions
17 --exclusions "${exclusions}" 20 --exclusions "${exclusions}"
18 #end if 21 #end if
19 #if $exclusions 22 #if $sem_sim_metric
20 --semantic-sim-metric "${sem_sim_metric}" 23 --semantic-sim-metric "${sem_sim_metric}"
21 #end if 24 #end if
22 ]]></command> 25 ]]></command>
23 <inputs> 26 <inputs>
24 <param type="data" name="input_ref_file" label="Input reference file" format="txt" help="Text file with reference cell labels" /> 27 <param type="data" name="input_ref_file" label="Input reference file" format="txt" help="Text file with reference cell labels" />
25 <param type="data" name="exclusions" format="yml" label="Exclusions file" help="YML file with excluded/unlabelled terms" /> 28 <param type="data" name="exclusions" format="yml" label="Exclusions file" help="YML file with excluded/unlabelled terms" />
26 <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" /> 29 <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" />
30 <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
27 <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" /> 31 <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />
28 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" /> 32 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
29 <param type="integer" name="num_iter" value='5' label="Number of iterations" help="Number of simulations to generate empirical CDF" /> 33 <param type="integer" name="num_iter" value='5' label="Number of iterations" help="Number of simulations to generate empirical CDF" />
30 <param type="data" name="ontology_graph" label="Ontology graph" format="obo" help="Ontology graph to run semantis similarity computations" /> 34 <param type="integer" name="sample_labs" value='50' label="Number of labels to sample" help="Numbre of labels to sample for each permutation" />
31 <param type="text" name="sem_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" /> 35 <param type="data" name="ontology_graph" label="Ontology graph" format="obo" optional="true" help="Ontology graph to run semantis similarity computations" />
36 <expand macro="sem_siml_options" />
32 </inputs> 37 </inputs>
33 <outputs> 38 <outputs>
34 <data name="output_list_path" format="rdata" /> 39 <data name="output_list_path" format="rdata" />
35 </outputs> 40 </outputs>
36 <tests> 41 <tests>