Mercurial > repos > ebi-gxa > ct_build_cell_ontology_dict

comparison ct_build_cell_ontology_dict.xml @ 5:512b239a11ad draft default tip

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:37:02 +0000
parents b51c48b16ffe
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4:b51c48b16ffe 5:512b239a11ad
1 <tool id="ct_build_cell_ontology_dict" name="Cell types - build cell ontology map" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 1 <tool id="ct_build_cell_ontology_dict" name="Cell types - build cell ontology map" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>Create a mapping from labels to CL terms</description> 2 <description>Create a mapping from labels to CL terms</description>
3 <macros> 3 <macros>
4 <import>ct_macros.xml</import> 4 <import>ct_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
25 #end if 25 #end if
26 ]]></command> 26 ]]></command>
27 <inputs> 27 <inputs>
28 <param type="data" name="input_sdrfs" label="Input SDRF tables" multiple="true" format="txt" help="Input SDRF tables" /> 28 <param type="data" name="input_sdrfs" label="Input SDRF tables" multiple="true" format="txt" help="Input SDRF tables" />
29 <param type="boolean" name="condensed_sdrf" checked="false" label="Condensed SDRF" help="Are the supplied SDRFs of condensed format?" /> 29 <param type="boolean" name="condensed_sdrf" checked="false" label="Condensed SDRF" help="Are the supplied SDRFs of condensed format?" />
30 <param type="text" name="barcode_col_name" label="Barcode column name" value="id" help="Name of the barcode field in provided SDRF files" /> 30 <param type="text" name="barcode_col_name" label="Barcode column name" value="id" help="Name of the barcode field in provided SDRF files">
31 <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" /> 31 <expand macro="sanitize_strings" />
32 <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)" /> 32 </param>
33 <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">
34 <expand macro="sanitize_strings" />
35 </param>
36 <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)">
37 <expand macro="sanitize_strings" />
38 </param>
33 </inputs> 39 </inputs>
34 <outputs> 40 <outputs>
35 <data name="output_dict_path" format="rdata" /> 41 <data name="output_dict_path" format="rdata" />
36 <data name="output_txt_path" format="txt" /> 42 <data name="output_txt_path" format="txt" />
37 </outputs> 43 </outputs>
38 <tests> 44 <tests>
39 <test> 45 <test>
40 <param name="input_sdrfs" value="SDRFs/ref_condensed_sdrf.tsv,SDRFs/ref_condensed_sdrf_1.tsv" /> 46 <param name="input_sdrfs" value="SDRFs/E-ENAD-27.condensed-sdrf.tsv,SDRFs/ref_condensed_sdrf.tsv,SDRFs/E-GEOD-81608.condensed-sdrf.tsv" />
41 <param name="condensed_sdrf" value="TRUE" /> 47 <param name="condensed_sdrf" value="TRUE" />
42 <output name="output_dict_path" file="label_cl_dict.rds" compare="sim_size" /> 48 <output name="output_dict_path" file="label_cl_dict.rds" compare="sim_size" />
43 </test> 49 </test>
44 </tests> 50 </tests>
45 <help><![CDATA[ 51 <help><![CDATA[