Mercurial > repos > ebi-gxa > ct_build_cell_ontology_dict
view ct_build_cell_ontology_dict.xml @ 5:512b239a11ad draft default tip
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author | ebi-gxa |
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date | Fri, 27 Nov 2020 13:37:02 +0000 |
parents | b51c48b16ffe |
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<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 --output-dict-path "${output_dict_path}" --output-text-path "${output_txt_path}" #if $condensed_sdrf --condensed-sdrf "${condensed_sdrf}" #end if #if $barcode_col_name --barcode-col-name "${barcode_col_name}" #end if #if $cell_label_col_name --cell-label-col-name "${cell_label_col_name}" #end if #if $cell_ontology_col_name --cell-ontology-col-name "${cell_ontology_col_name}" #end if ]]></command> <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"> <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" /> <data name="output_txt_path" format="txt" /> </outputs> <tests> <test> <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> </tests> <help><![CDATA[ @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations" /> </tool>