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comparison table-union.xml @ 14:1af2524f48b7 tip

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author jpayne
date Tue, 30 Oct 2018 16:18:02 -0400
parents 15230438f7f5
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13:746091a78780 14:1af2524f48b7
2 <description>by combining their rows and unionizing columns</description> 2 <description>by combining their rows and unionizing columns</description>
3 <requirements> 3 <requirements>
4 <!-- <requirement type="package" version="3.4">python</requirement> --> 4 <!-- <requirement type="package" version="3.4">python</requirement> -->
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 python $__tool_directory__/table-union.py 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 $__tool_directory__/table-union.py "$union"
8 #for $table in $tables 13 #for $table in $tables
9 $table 14 $table
10 #end for 15 #end for
11 > $combined_table 16 > $combined_table
12 ]]></command> 17 ]]></command>
13 <inputs> 18 <inputs>
14 <param name="tables" type="data_collection" format="tsv" collection_type="list" /> 19 <param name="union" type="boolean" label="Attempt to unionize on an autodetected key column" checked="false" falsevalue="" />
20 <conditional name="input_type">
21 <param name="source_select" type="select" label="Mode">
22 <option value="two">Combine two tables</option>
23 <option value="collection">Combine a collection of tables</option>
24 </param>
25 <when value="collection">
26 <param name="tables" type="data_collection" format="tabular,tsv" collection_type="list" />
27 </when>
28 <when value="two">
29 <param name="table_1" type="data" format="tabular,tsv" />
30 <param name="table_2" type="data" format="tabular,tsv" />
31 </when>
32 </conditional>
15 </inputs> 33 </inputs>
16 <outputs> 34 <outputs>
17 <data name="combined_table" format="tsv" label="Combined table" /> 35 <data name="combined_table" format="tsv" label="Combined table" />
18 </outputs> 36 </outputs>
19 37
20 <tests> 38 <tests>
21 <test> 39 <test>
40 <param name="source_select" value="collection" />
41 <param name="union" value="true" />
22 <param name="tables"> 42 <param name="tables">
23 <collection type="list"> 43 <collection type="list">
24 <element name="1" value="dingbat.tsv" /> 44 <element name="1" value="dingbat.tsv" />
25 <element name="2" value="loki.tsv" /> 45 <element name="2" value="loki.tsv" />
26 </collection> 46 </collection>
27 </param> 47 </param>
28 <output name="combined_table" value="combined.tsv" /> 48 <output name="combined_table" value="combined.tsv" />
49 </test>
50 <test>
51 <param name="source_select" value="two" />
52 <param name="union" value="false" />
53 <param name="table_1" value="dingbat.tsv" />
54 <param name="table_2" value="loki.tsv" />
55 <output name="combined_table" value="no_union.tsv" />
29 </test> 56 </test>
30 </tests> 57 </tests>
31 <help><![CDATA[ 58 <help><![CDATA[
32 Concatenate a collection of TSV files wile preserving and unionizing headers. 59 Concatenate a collection of TSV files wile preserving and unionizing headers.
33 ]]></help> 60 ]]></help>