| Next changeset 1:9d5e6a4ec5b5 (2020-04-24) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2" |
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added:
ct_get_empirical_dist.xml ct_macros.xml |
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| diff -r 000000000000 -r 196cc72cebd1 ct_get_empirical_dist.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ct_get_empirical_dist.xml Wed Apr 08 11:34:54 2020 -0400 |
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| @@ -0,0 +1,43 @@ +<tool id="ct_get_empirical_dist" name="Cell types - get empirical distribution" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>Get empirical distribution for tool performance table</description> + <macros> + <import>ct_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + + ln -s $'${ontology_graph}' cl-basic.obo; + + 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> + <inputs> + <param type="data" name="input_ref_file" label="Input reference file" format="tsv" 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="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="integer" name="num_cores" value='4' label="Number of cores" help="Number of cores to run the process" /> + <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" /> + </inputs> + <outputs> + <data name="output_list_path" format="rdata" /> + </outputs> + <tests> + <test> + <param name="input_ref_file" value="reference_sdrf.tsv" /> + <param name="label_col_ref" value="Sample.Characteristic.cell.type." /> + <param name="ontology_graph" value="cl-basic.obo" /> + <param name="exclusions" value="exclusions.yml" /> + <param name="parallel" value="TRUE" /> + <param name="lab_cl_mapping" value="label_cl_dict.rds" /> + <output name="output_list_path" file="empirical_dist_list.rds" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ + @HELP@ + + @VERSION_HISTORY@ + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 196cc72cebd1 ct_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ct_macros.xml Wed Apr 08 11:34:54 2020 -0400 |
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| @@ -0,0 +1,35 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.0</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> + <yield/> + </requirements> + </xml> + <xml name="version"> + <version_command><![CDATA[ + conda list | grep cell-types-analysis | egrep -o [0-9]\.[0-9]\.[0-9] + ]]></version_command> + </xml> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** +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/. + ]]></token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{github-cell-types-analysis.git, + author = {Andrey Solovyev, EBI Gene Expression Team}, + year = {2020}, + title = {Suite of scripts for analysis of scRNA-seq cell type classification tool outputs}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/cell-types-analysis.git}, + } + </citation> + <yield /> + </citations> + </xml> +</macros> \ No newline at end of file |