| Previous changeset 4:b51c48b16ffe (2020-06-17) |
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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_build_cell_ontology_dict.xml ct_macros.xml |
| b |
| diff -r b51c48b16ffe -r 512b239a11ad ct_build_cell_ontology_dict.xml --- a/ct_build_cell_ontology_dict.xml Wed Jun 17 12:31:51 2020 -0400 +++ b/ct_build_cell_ontology_dict.xml Fri Nov 27 13:37:02 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="ct_build_cell_ontology_dict" name="Cell types - build cell ontology map" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="ct_build_cell_ontology_dict" name="Cell types - build cell ontology map" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>Create a mapping from labels to CL terms</description> <macros> <import>ct_macros.xml</import> @@ -27,9 +27,15 @@ <inputs> <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="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)" /> + <param type="text" name="barcode_col_name" label="Barcode column name" value="id" help="Name of the barcode field in provided SDRF files"> + <expand macro="sanitize_strings" /> + </param> + <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"> + <expand macro="sanitize_strings" /> + </param> + <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)"> + <expand macro="sanitize_strings" /> + </param> </inputs> <outputs> <data name="output_dict_path" format="rdata" /> @@ -37,7 +43,7 @@ </outputs> <tests> <test> - <param name="input_sdrfs" value="SDRFs/ref_condensed_sdrf.tsv,SDRFs/ref_condensed_sdrf_1.tsv" /> + <param name="input_sdrfs" value="SDRFs/E-ENAD-27.condensed-sdrf.tsv,SDRFs/ref_condensed_sdrf.tsv,SDRFs/E-GEOD-81608.condensed-sdrf.tsv" /> <param name="condensed_sdrf" value="TRUE" /> <output name="output_dict_path" file="label_cl_dict.rds" compare="sim_size" /> </test> |
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| diff -r b51c48b16ffe -r 512b239a11ad ct_macros.xml --- a/ct_macros.xml Wed Jun 17 12:31:51 2020 -0400 +++ b/ct_macros.xml Fri Nov 27 13:37:02 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"> |