| Previous changeset 5:36eab91e0ff5 (2020-07-13) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19" |
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modified:
ct_get_empirical_dist.xml ct_macros.xml |
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| diff -r 36eab91e0ff5 -r 14eb5128af69 ct_get_empirical_dist.xml --- a/ct_get_empirical_dist.xml Mon Jul 13 07:24:39 2020 -0400 +++ b/ct_get_empirical_dist.xml Fri Nov 27 13:38:33 2020 +0000 |
| [ |
| @@ -1,22 +1,16 @@ -<tool id="ct_get_empirical_dist" name="Cell types - get empirical distribution" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> - <description>Get empirical distribution for tool performance table</description> +<tool id="ct_get_empirical_dist" name="Cell types - get empirical distribution" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>for tool performance table</description> <macros> <import>ct_macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - 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} --output-path "${output_list_path}" + get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}" --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --tmpdir ./ --output-path "${output_list_path}" - #if $parallel - --parallel "${parallel}" - #end if #if $ontology_graph --ontology-graph "${ontology_graph}" #end if - #if $tmpdir - --tmpdir "${tmpdir}" - #end if #if $sample_labs --sample-labs "${sample_labs}" #end if @@ -31,12 +25,12 @@ <inputs> <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" optional="true" 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="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file"> + <expand macro="sanitize_strings" /> + </param> <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="sample_labs" value='50' label="Number of labels to sample" help="Numbre of labels to sample for each permutation" /> + <param type="integer" name="sample_labs" value='50' label="Number of labels to sample" help="Number 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> @@ -46,10 +40,9 @@ <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="label_col_ref" value='Sample Characteristic[cell type]' /> <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> |
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| diff -r 36eab91e0ff5 -r 14eb5128af69 ct_macros.xml --- a/ct_macros.xml Mon Jul 13 07:24:39 2020 -0400 +++ b/ct_macros.xml Fri Nov 27 13:38:33 2020 +0000 |
| [ |
| @@ -1,10 +1,10 @@ <macros> - <token name="@TOOL_VERSION@">1.1.0</token> + <token name="@TOOL_VERSION@">1.1.1</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="0.1.1">cell-types-analysis</requirement> + <requirement type="package" version="0.1.9">cell-types-analysis</requirement> <yield/> </requirements> </xml> @@ -15,6 +15,7 @@ </xml> <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +0.1.6+galaxy0: Add removing non-alphanumeric characters from labels in metadata files 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> @@ -34,6 +35,17 @@ <option value="resnik">resnik</option> </param> </xml> + <xml name="sanitize_strings"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits"> + <add value="_" /> + <add value="-" /> + <add value="[" /> + <add value="]" /> + <add value=" " /> + </valid> + </sanitizer> + </xml> <xml name="citations"> <citations> <citation type="bibtex"> |