Mercurial > repos > ebi-gxa > ct_build_cell_ontology_dict

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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
children
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1 <tool id="ct_build_cell_ontology_dict" name="Cell types - build cell ontology map" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>Create a mapping from labels to CL terms</description>
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3 <macros>
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4 <import>ct_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 mkdir -p input_dir;
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9 #for $sdrf in $input_sdrfs:
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10 cp '$sdrf' input_dir/;
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11 #end for
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12
1
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13 build_cell_ontology_dict.R --input-dir input_dir --output-dict-path "${output_dict_path}" --output-text-path "${output_txt_path}"
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14 #if $condensed_sdrf
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15 --condensed-sdrf "${condensed_sdrf}"
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16 #end if
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17 #if $barcode_col_name
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18 --barcode-col-name "${barcode_col_name}"
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19 #end if
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20 #if $cell_label_col_name
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21 --cell-label-col-name "${cell_label_col_name}"
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22 #end if
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23 #if $cell_ontology_col_name
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24 --cell-ontology-col-name "${cell_ontology_col_name}"
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25 #end if
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26 ]]></command>
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27 <inputs>
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28 <param type="data" name="input_sdrfs" label="Input SDRF tables" multiple="true" format="txt" help="Input SDRF tables" />
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29 <param type="boolean" name="condensed_sdrf" checked="false" label="Condensed SDRF" help="Are the supplied SDRFs of condensed format?" />
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30 <param type="text" name="barcode_col_name" label="Barcode column name" value="id" help="Name of the barcode field in provided SDRF files">
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31 <expand macro="sanitize_strings" />
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32 </param>
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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">
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34 <expand macro="sanitize_strings" />
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35 </param>
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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)">
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37 <expand macro="sanitize_strings" />
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38 </param>
0
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39 </inputs>
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40 <outputs>
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41 <data name="output_dict_path" format="rdata" />
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42 <data name="output_txt_path" format="txt" />
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43 </outputs>
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44 <tests>
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45 <test>
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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" />
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47 <param name="condensed_sdrf" value="TRUE" />
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48 <output name="output_dict_path" file="label_cl_dict.rds" compare="sim_size" />
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 @HELP@
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53
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54 @VERSION_HISTORY@
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55 ]]></help>
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56 <expand macro="citations" />
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57 </tool>