| Previous changeset 3:982a151b2960 (2020-04-27) Next changeset 5:512b239a11ad (2020-11-27) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1" |
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modified:
ct_build_cell_ontology_dict.xml ct_macros.xml |
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| diff -r 982a151b2960 -r b51c48b16ffe ct_build_cell_ontology_dict.xml --- a/ct_build_cell_ontology_dict.xml Mon Apr 27 11:13:32 2020 -0400 +++ b/ct_build_cell_ontology_dict.xml Wed Jun 17 12:31:51 2020 -0400 |
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| @@ -28,7 +28,7 @@ <param type="data" name="input_sdrfs" label="Input SDRF tables" multiple="true" format="txt" help="Input SDRF tables" /> <param type="boolean" name="condensed_sdrf" checked="false" label="Condensed SDRF" help="Are the supplied SDRFs of condensed format?" /> <param type="text" name="barcode_col_name" label="Barcode column name" value="id" help="Name of the barcode field in provided SDRF files" /> - <param type="text" name="cell_label_col_name" label="Cell label column name" value="cell.type" help="Name of the cell label field name in provided SDRF files" /> + <param type="text" name="cell_label_col_name" label="Cell label column name" value="inferred cell type" help="Name of the cell label field name in provided SDRF files" /> <param type="text" name="cell_ontology_col_name" label="Cell ontology column name" value="cell.type.ontology" help="Name of the cell ontology terms column in SDRF files (must be identical across all files)" /> </inputs> <outputs> |
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| diff -r 982a151b2960 -r b51c48b16ffe ct_macros.xml --- a/ct_macros.xml Mon Apr 27 11:13:32 2020 -0400 +++ b/ct_macros.xml Wed Jun 17 12:31:51 2020 -0400 |
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| @@ -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"> |