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comparison qiime2/qiime_feature-table_merge.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_merge" name="qiime feature-table merge" version="2018.4">
3 <description> - Combine multiple tables</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime feature-table merge
10
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 $file_list
17 #end def
18
19
20 --i-tables=$list_dict_to_string($input_files_itables)
21
22 #if str($cmdconfig) != 'None':
23 --cmd-config=$cmdconfig
24 #end if
25 --o-merged-table=omergedtable
26 #if str($poverlapmethod) != 'None':
27 --p-overlap-method=$poverlapmethod
28 #end if
29 ;
30 cp omergedtable.qza $omergedtable;
31 ]]>
32 </command>
33 <inputs>
34 <repeat name="input_files_itables" optional="False" title="--i-tables">
35 <param format="qza,no_unzip.zip" label="--i-tables: PATH List[FeatureTable[Frequency]] The collection of feature tables to be merged. [required]" name="additional_input" type="data"/>
36 </repeat>
37 <param label="--p-overlap-method: Method for handling overlapping ids.
38 [default: error_on_overlapping_sample]" name="poverlapmethod" optional="True" type="select">
39 <option selected="True" value="None">Selection is Optional</option>
40 <option value="error_on_overlapping_feature">error_on_overlapping_feature</option>
41 <option value="error_on_overlapping_sample">error_on_overlapping_sample</option>
42 <option value="sum">sum</option>
43 </param>
44 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
45 </inputs>
46 <outputs>
47 <data format="qza" label="${tool.name} on ${on_string}: merged-table.qza" name="omergedtable"/>
48 </outputs>
49 <help>
50 <![CDATA[
51 Combine multiple tables
52 ------------------------
53
54 Combines feature tables using the `overlap_method` provided.
55
56 Parameters
57 ----------
58 tables : List[FeatureTable[Frequency]]
59 The collection of feature tables to be merged.
60 overlap_method : Str % Choices({'error_on_overlapping_feature', 'error_on_overlapping_sample', 'sum'}), optional
61 Method for handling overlapping ids.
62
63 Returns
64 -------
65 merged_table : FeatureTable[Frequency]
66 The resulting merged feature table.
67 ]]>
68 </help>
69 <macros>
70 <import>qiime_citation.xml</import>
71 </macros>
72 <expand macro="qiime_citation" />
73 </tool>