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comparison qiime2/qiime_feature-table_merge.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_merge" name="qiime feature-table merge" version="2019.4">
3 <description> - Combine multiple tables</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime feature-table merge
9
10 #def list_dict_to_string(list_dict):
11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
12 #for d in list_dict[1:]:
13 #set $file_list = $file_list + ' --i-tables=' + d['additional_input'].__getattr__('file_name')
14 #end for
15 #return $file_list
16 #end def
17 --i-tables=$list_dict_to_string($input_files_itables)
18
19
20 #if str($poverlapmethod) != 'None':
21 --p-overlap-method=$poverlapmethod
22 #end if
23
24
25 --o-merged-table=omergedtable
26 ;
27 cp omergedtable.qza $omergedtable
28 ]]></command>
29 <inputs>
30 <repeat name="input_files_itables" optional="False" title="--i-tables">
31 <param format="qza,no_unzip.zip" label="--i-tables: PATH List[FeatureTable[Frequency]] The collection of feature tables to be merged. [required]" name="additional_input" type="data"/>
32 </repeat>
33
34 <param label="--p-overlap-method: " name="poverlapmethod" optional="True" type="select">
35 <option selected="True" value="None">Selection is Optional</option>
36 <option value="error_on_overlapping_sample">error_on_overlapping_sample</option>
37 <option value="error_on_overlapping_feature">error_on_overlapping_feature</option>
38 <option value="sum">sum</option>
39 </param>
40 </inputs>
41 <outputs>
42 <data format="qza" label="${tool.name} on ${on_string}: mergedtable.qza" name="omergedtable"/>
43 </outputs>
44 <help><![CDATA[
45 Combine multiple tables
46 #######################
47
48 Combines feature tables using the `overlap_method` provided.
49
50 Parameters
51 ----------
52 tables : List[FeatureTable[Frequency]]
53 The collection of feature tables to be merged.
54 overlap_method : Str % Choices('error_on_overlapping_sample', 'error_on_overlapping_feature', 'sum'), optional
55 Method for handling overlapping ids.
56
57 Returns
58 -------
59 merged_table : FeatureTable[Frequency]
60 The resulting merged feature table.
61 ]]></help>
62 <macros>
63 <import>qiime_citation.xml</import>
64 </macros>
65 <expand macro="qiime_citation"/>
66 </tool>