Mercurial > repos > ebi-gxa > ct_build_cell_ontology_dict

comparison ct_build_cell_ontology_dict.xml @ 1:7086be9e707e draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
author ebi-gxa
date Fri, 24 Apr 2020 11:20:33 -0400
parents 406d293e567e
children f1f720a9b679
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0:406d293e567e 1:7086be9e707e
8 mkdir -p input_dir; 8 mkdir -p input_dir;
9 #for $sdrf in $input_sdrfs: 9 #for $sdrf in $input_sdrfs:
10 cp '$sdrf' input_dir/; 10 cp '$sdrf' input_dir/;
11 #end for 11 #end for
12 12
13 build_cell_ontology_dict.R --input-dir input_dir --condensed-sdrf "${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 "${output_txt_path}" ]]></command> 13 build_cell_ontology_dict.R --input-dir input_dir --output-dict-path "${output_dict_path}" --output-text-path "${output_txt_path}"
14 #if $condensed_sdrf
15 --condensed-sdrf "${condensed_sdrf}"
16 #end if
17 #if $barcode_col_name
18 --barcode-col-name "${barcode_col_name}"
19 #end if
20 #if $cell_label_col_name
21 --cell-label-col-name "${cell_label_col_name}"
22 #end if
23 #if $cell_ontology_col_name
24 --cell-ontology-col-name "${cell_ontology_col_name}"
25 #end if
26 ]]></command>
14 <inputs> 27 <inputs>
15 <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="tsv" help="Input SDRF tables" />
16 <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?" />
17 <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" />
18 <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" />