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author jpayne
date Mon, 08 Dec 2025 15:03:06 +0000
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1 <tool id="table-union" name="Table Union: Merge tabular datasets" version="0.1.0">
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2 <description>by combining their rows and unionizing columns</description>
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3 <requirements>
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4 <container type="docker">cfsanbiostatistics/tableops:latest</container>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #if $input_type.source_select == 'two'
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8 #set tables=($table_1, $table_2)
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9 #else
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10 #set tables=$input_type.tables
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11 #end if
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12 python $__tool_directory__/table-union.py $adv.union $adv.tuple_mode
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13 #for $table in $tables
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14 $table
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15 #end for
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16 > $combined_table
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17 ]]></command>
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18 <inputs>
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19 <conditional name="input_type">
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20 <param name="source_select" type="select" label="Mode">
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21 <option value="two">Combine two tables</option>
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22 <option value="collection">Combine a collection of tables</option>
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23 </param>
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24 <when value="collection">
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25 <param name="tables" type="data_collection" format="tabular,tsv" collection_type="list" optional="true" />
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26 </when>
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27 <when value="two">
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28 <param name="table_1" type="data" format="tabular,tsv" optional="true" />
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29 <param name="table_2" type="data" format="tabular,tsv" optional="true"/>
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30 </when>
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31 </conditional>
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32 <!-- Advanced options, click to show -->
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33 <section name="adv" title="Advanced options">
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34 <param name="union" type="boolean" label="Attempt to unionize on an autodetected key column" checked="false" truevalue="--unionize" falsevalue="" />
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35 <param name="tuple_mode" type="boolean" label="For tables with inconsistent headers - unionize by column order instead of column " checked="false" truevalue="--tuple" falsevalue="" />
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36 </section>
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37 </inputs>
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38 <outputs>
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39 <data name="combined_table" format="tsv" label="Combined table" />
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40 </outputs>
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41
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42 <tests>
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43 <test>
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44 <conditional name="input_type">
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45 <param name="source_select" value="collection" />
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46
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47 <param name="tables">
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48 <collection type="list">
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49 <element name="table_1" value="dingbat.tsv" />
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50 <element name="table_2" value="loki.tsv" />
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51 </collection>
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52 </param>
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53 </conditional>
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54 <section name="adv">
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55 <param name="union" value="true" />
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56 </section>
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57 <output name="combined_table" value="combined.tsv" />
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58 </test>
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59 <test>
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60 <conditional name="input_type">
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61 <param name="source_select" value="two" />
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62
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63 <param name="table_1" value="dingbat.tsv" />
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64 <param name="table_2" value="loki.tsv" />
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65 </conditional>
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66 <section name="adv">
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67 <param name="union" value="false" />
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68 </section>
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69 <output name="combined_table" value="no_union.tsv" />
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70 </test>
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71 <test>
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72 <conditional name="input_type">
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73 <param name="source_select" value="two" />
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74
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75 <param name="table_1" value="dingbat.tsv" />
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76 <param name="table_2" value="loki.tsv" />
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77 </conditional>
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78 <section name="adv">
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79 <param name="tuple_mode" value="true" />
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80 </section>
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81 <output name="combined_table" value="tuple.tsv" />
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85 Concatenate a collection of TSV files wile preserving and unionizing headers.
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86 ]]></help>
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87
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88 <citations>
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89 <citation type="bibtex">
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90 @misc{githubsometool,
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91 author = {Payne, Justin},
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92 year = {2022},
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93 title = {tableops},
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94 publisher = {GitHub},
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95 journal = {GitHub repository},
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96 url = {https://github.com/CFSAN-Biostatistics/table-ops},
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97 }</citation>
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98 </citations>
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99 </tool>