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comparison qiime2-2020.8/qiime_feature-table_merge.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_merge" name="qiime feature-table merge"
3 version="2020.8">
4 <description>Combine multiple tables</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime feature-table merge
10 # if $input_files_itables:
11 # def list_dict_to_string(list_dict):
12 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
13 # for d in list_dict[1:]:
14 # set $file_list = $file_list + ' --i-tables=' + d['additional_input'].__getattr__('file_name')
15 # end for
16 # return $file_list
17 # end def
18 --i-tables=$list_dict_to_string($input_files_itables)
19 # end if
20
21 #if str($poverlapmethod) != 'None':
22 --p-overlap-method=$poverlapmethod
23 #end if
24
25 --o-merged-table=omergedtable
26
27 #if str($examples) != 'None':
28 --examples=$examples
29 #end if
30
31 ;
32 cp omergedtable.qza $omergedtable
33
34 ]]></command>
35 <inputs>
36 <repeat name="input_files_itables" optional="False" title="--i-tables">
37 <param format="qza,no_unzip.zip" label="--i-tables: ARTIFACTS... List[FeatureTable[Frequency]] The collection of feature tables to be merged. [required]" name="additional_input" optional="False" type="data" />
38 </repeat>
39 <param label="--p-overlap-method: " name="poverlapmethod" optional="True" type="select">
40 <option selected="True" value="None">Selection is Optional</option>
41 <option value="error_on_overlapping_sample">error_on_overlapping_sample</option>
42 <option value="error_on_overlapping_feature">error_on_overlapping_feature</option>
43 <option value="sum">sum</option>
44 </param>
45 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
46
47 </inputs>
48
49 <outputs>
50 <data format="qza" label="${tool.name} on ${on_string}: mergedtable.qza" name="omergedtable" />
51
52 </outputs>
53
54 <help><![CDATA[
55 Combine multiple tables
56 ###############################################################
57
58 Combines feature tables using the `overlap_method` provided.
59
60 Parameters
61 ----------
62 tables : List[FeatureTable[Frequency]]
63 The collection of feature tables to be merged.
64 overlap_method : Str % Choices('error_on_overlapping_sample', 'error_on_overlapping_feature', 'sum'), optional
65 Method for handling overlapping ids.
66
67 Returns
68 -------
69 merged_table : FeatureTable[Frequency]
70 The resulting merged feature table.
71 ]]></help>
72 <macros>
73 <import>qiime_citation.xml</import>
74 </macros>
75 <expand macro="qiime_citation"/>
76 </tool>