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planemo upload commit 9cc4dc1db55299bf92ec6bd359161ece4592bd16-dirty
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">
2 <description>by combining their rows and unionizing columns</description>
3 <requirements>
4 <container type="docker">cfsanbiostatistics/tableops:latest</container>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 #if $input_type.source_select == 'two'
8 #set tables=($table_1, $table_2)
9 #else
10 #set tables=$input_type.tables
11 #end if
12 python $__tool_directory__/table-union.py $adv.union $adv.tuple_mode
13 #for $table in $tables
14 $table
15 #end for
16 > $combined_table
17 ]]></command>
18 <inputs>
19 <conditional name="input_type">
20 <param name="source_select" type="select" label="Mode">
21 <option value="two">Combine two tables</option>
22 <option value="collection">Combine a collection of tables</option>
23 </param>
24 <when value="collection">
25 <param name="tables" type="data_collection" format="tabular,tsv" collection_type="list" optional="true" />
26 </when>
27 <when value="two">
28 <param name="table_1" type="data" format="tabular,tsv" optional="true" />
29 <param name="table_2" type="data" format="tabular,tsv" optional="true"/>
30 </when>
31 </conditional>
32 <!-- Advanced options, click to show -->
33 <section name="adv" title="Advanced options">
34 <param name="union" type="boolean" label="Attempt to unionize on an autodetected key column" checked="false" truevalue="--unionize" falsevalue="" />
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="" />
36 </section>
37 </inputs>
38 <outputs>
39 <data name="combined_table" format="tsv" label="Combined table" />
40 </outputs>
41
42 <tests>
43 <test>
44 <conditional name="input_type">
45 <param name="source_select" value="collection" />
46
47 <param name="tables">
48 <collection type="list">
49 <element name="table_1" value="dingbat.tsv" />
50 <element name="table_2" value="loki.tsv" />
51 </collection>
52 </param>
53 </conditional>
54 <section name="adv">
55 <param name="union" value="true" />
56 </section>
57 <output name="combined_table" value="combined.tsv" />
58 </test>
59 <test>
60 <conditional name="input_type">
61 <param name="source_select" value="two" />
62
63 <param name="table_1" value="dingbat.tsv" />
64 <param name="table_2" value="loki.tsv" />
65 </conditional>
66 <section name="adv">
67 <param name="union" value="false" />
68 </section>
69 <output name="combined_table" value="no_union.tsv" />
70 </test>
71 <test>
72 <conditional name="input_type">
73 <param name="source_select" value="two" />
74
75 <param name="table_1" value="dingbat.tsv" />
76 <param name="table_2" value="loki.tsv" />
77 </conditional>
78 <section name="adv">
79 <param name="tuple_mode" value="true" />
80 </section>
81 <output name="combined_table" value="tuple.tsv" />
82 </test>
83 </tests>
84 <help><![CDATA[
85 Concatenate a collection of TSV files wile preserving and unionizing headers.
86 ]]></help>
87
88 <citations>
89 <citation type="bibtex">
90 @misc{githubsometool,
91 author = {Payne, Justin},
92 year = {2022},
93 title = {tableops},
94 publisher = {GitHub},
95 journal = {GitHub repository},
96 url = {https://github.com/CFSAN-Biostatistics/table-ops},
97 }</citation>
98 </citations>
99 </tool>