Mercurial > repos > ebi-gxa > ct_build_cell_ontology_dict

comparison ct_build_cell_ontology_dict.xml @ 0:406d293e567e draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
author ebi-gxa
date Wed, 08 Apr 2020 11:35:35 -0400
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children 7086be9e707e
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-1:000000000000 0:406d293e567e
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>
3 <macros>
4 <import>ct_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p input_dir;
9 #for $sdrf in $input_sdrfs:
10 cp '$sdrf' input_dir/;
11 #end for
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>
14 <inputs>
15 <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?" />
17 <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" />
19 <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)" />
20 </inputs>
21 <outputs>
22 <data name="output_dict_path" format="rdata" />
23 <data name="output_txt_path" format="tsv" />
24 </outputs>
25 <tests>
26 <test>
27 <param name="input_sdrfs" value="SDRFs/ref_condensed_sdrf.tsv,SDRFs/ref_condensed_sdrf_1.tsv" />
28 <param name="condensed_sdrf" value="TRUE" />
29 <output name="output_dict_path" file="label_cl_dict.rds" compare="sim_size" />
30 </test>
31 </tests>
32 <help><![CDATA[
33 @HELP@
34
35 @VERSION_HISTORY@
36 ]]></help>
37 <expand macro="citations" />
38 </tool>