|
0
|
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 </tool>
|
