| Previous changeset 3:ce70358b0fe3 (2020-04-27) Next changeset 5:36eab91e0ff5 (2020-07-13) |
|
Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1" |
|
modified:
ct_get_empirical_dist.xml ct_macros.xml |
| b |
| diff -r ce70358b0fe3 -r 5bf2827cd314 ct_get_empirical_dist.xml --- a/ct_get_empirical_dist.xml Mon Apr 27 11:12:46 2020 -0400 +++ b/ct_get_empirical_dist.xml Wed Jun 17 12:30:58 2020 -0400 |
| b |
| @@ -13,10 +13,13 @@ #if $parallel --parallel "${parallel}" #end if + #if $sample_labs + --sample-labs "${sample_labs}" + #end if #if $exclusions --exclusions "${exclusions}" #end if - #if $exclusions + #if $sem_sim_metric --semantic-sim-metric "${sem_sim_metric}" #end if ]]></command> @@ -24,11 +27,13 @@ <param type="data" name="input_ref_file" label="Input reference file" format="txt" help="Text file with reference cell labels" /> <param type="data" name="exclusions" format="yml" label="Exclusions file" help="YML file with excluded/unlabelled terms" /> <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" /> + <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" /> <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" /> <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" /> <param type="integer" name="num_iter" value='5' label="Number of iterations" help="Number of simulations to generate empirical CDF" /> - <param type="data" name="ontology_graph" label="Ontology graph" format="obo" help="Ontology graph to run semantis similarity computations" /> - <param type="text" name="sem_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" /> + <param type="integer" name="sample_labs" value='50' label="Number of labels to sample" help="Numbre of labels to sample for each permutation" /> + <param type="data" name="ontology_graph" label="Ontology graph" format="obo" optional="true" help="Ontology graph to run semantis similarity computations" /> + <expand macro="sem_siml_options" /> </inputs> <outputs> <data name="output_list_path" format="rdata" /> |
| b |
| diff -r ce70358b0fe3 -r 5bf2827cd314 ct_macros.xml --- a/ct_macros.xml Mon Apr 27 11:12:46 2020 -0400 +++ b/ct_macros.xml Wed Jun 17 12:30:58 2020 -0400 |
| [ |
| @@ -1,10 +1,10 @@ <macros> - <token name="@TOOL_VERSION@">1.0.0</token> + <token name="@TOOL_VERSION@">1.1.0</token> <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/cell-types-analysis</token> <token name="@PROFILE@">18.01</token> <xml name="requirements"> <requirements> - <requirement type="package" version="0.0.8">cell-types-analysis</requirement> + <requirement type="package" version="0.1.1">cell-types-analysis</requirement> <yield/> </requirements> </xml> @@ -18,6 +18,22 @@ 0.0.5+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. 0.0.5+galaxy1: Standardise input/output format into .txt. ]]></token> + <xml name="sem_siml_options"> + <param type="select" name="sem_siml_metric" label="Semantic similarity metric" help="What semantic similarity metric should be used? NB: if include-sem-siml is set to True, make sure to use a metric that is in the [0;1] interval. See https://www.bioconductor.org/packages/release/bioc/html/Onassis.html for more detail."> + <option value="lin" selected="true">lin</option> + <option value="jaccard">jaccard</option> + <option value="jc_norm">jc_norm</option> + <option value="schlicker">schlicker</option> + <option value="edge_resnik">edge_resnik</option> + <option value="sim">sim</option> + <option value="edge_leachod">edge_leachod</option> + <option value="edge_slimani">edge_slimani</option> + <option value="edge_wupalmer">edge_wupalmer</option> + <option value="edge_rada_lca">edge_rada_lca</option> + <option value="edge_li">edge_li</option> + <option value="resnik">resnik</option> + </param> + </xml> <xml name="citations"> <citations> <citation type="bibtex"> |