Mercurial > repos > ebi-gxa > ct_build_cell_ontology_dict

annotate 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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406d293e567e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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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 <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" />
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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)" />
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33 </inputs>
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34 <outputs>
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35 <data name="output_dict_path" format="rdata" />
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36 <data name="output_txt_path" format="txt" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="input_sdrfs" value="SDRFs/ref_condensed_sdrf.tsv,SDRFs/ref_condensed_sdrf_1.tsv" />
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41 <param name="condensed_sdrf" value="TRUE" />
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42 <output name="output_dict_path" file="label_cl_dict.rds" compare="sim_size" />
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46 @HELP@
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47
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48 @VERSION_HISTORY@
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49 ]]></help>
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50 <expand macro="citations" />
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51 </tool>