Mercurial > repos > ebi-gxa > ct_build_cell_ontology_dict

comparison ct_build_cell_ontology_dict.xml @ 2:f1f720a9b679 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
author ebi-gxa
date Mon, 27 Apr 2020 09:29:47 -0400
parents 7086be9e707e
children 982a151b2960
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1:7086be9e707e 2:f1f720a9b679
23 #if $cell_ontology_col_name 23 #if $cell_ontology_col_name
24 --cell-ontology-col-name "${cell_ontology_col_name}" 24 --cell-ontology-col-name "${cell_ontology_col_name}"
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="tsv" 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="cell.type" help="Name of the cell label field name in provided SDRF files" /> 31 <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" />
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 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)" />
33 </inputs> 33 </inputs>
34 <outputs> 34 <outputs>
35 <data name="output_dict_path" format="rdata" /> 35 <data name="output_dict_path" format="rdata" />
36 <data name="output_txt_path" format="tsv" /> 36 <data name="output_txt_path" format="txt" />
37 </outputs> 37 </outputs>
38 <tests> 38 <tests>
39 <test> 39 <test>
40 <param name="input_sdrfs" value="SDRFs/ref_condensed_sdrf.tsv,SDRFs/ref_condensed_sdrf_1.tsv" /> 40 <param name="input_sdrfs" value="SDRFs/ref_condensed_sdrf.tsv,SDRFs/ref_condensed_sdrf_1.tsv" />
41 <param name="condensed_sdrf" value="TRUE" /> 41 <param name="condensed_sdrf" value="TRUE" />