| Next changeset 1:7086be9e707e (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_build_cell_ontology_dict.xml ct_macros.xml |
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| diff -r 000000000000 -r 406d293e567e ct_build_cell_ontology_dict.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ct_build_cell_ontology_dict.xml Wed Apr 08 11:35:35 2020 -0400 |
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| @@ -0,0 +1,38 @@ +<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> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + mkdir -p input_dir; + #for $sdrf in $input_sdrfs: + cp '$sdrf' input_dir/; + #end for + + build_cell_ontology_dict.R --input-dir input_dir --condensed-sdrf "${condensed_sdrf}" --barcode-col-name "${barcode_col_name}" --cell-label-col-name "${cell_label_col_name}" --cell-ontology-col-name "${cell_ontology_col_name}" --output-dict-path "${output_dict_path}" --output-text-path "${output_txt_path}" ]]></command> + <inputs> + <param type="data" name="input_sdrfs" label="Input SDRF tables" multiple="true" format="tsv" 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_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> + <data name="output_dict_path" format="rdata" /> + <data name="output_txt_path" format="tsv" /> + </outputs> + <tests> + <test> + <param name="input_sdrfs" value="SDRFs/ref_condensed_sdrf.tsv,SDRFs/ref_condensed_sdrf_1.tsv" /> + <param name="condensed_sdrf" value="TRUE" /> + <output name="output_dict_path" file="label_cl_dict.rds" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ + @HELP@ + + @VERSION_HISTORY@ + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 406d293e567e ct_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ct_macros.xml Wed Apr 08 11:35:35 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 |