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comparison qiime2/qiime_feature-table_merge.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_merge" name="qiime feature-table merge" version="2019.7"> 2 <tool id="qiime_feature-table_merge" name="qiime feature-table merge"
3 <description> - Combine multiple tables</description> 3 version="2020.8">
4 <requirements> 4 <description>Combine multiple tables</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime feature-table merge 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
9 20
10 #if $input_files_itables: 21 #if str($poverlapmethod) != 'None':
11 #def list_dict_to_string(list_dict): 22 --p-overlap-method=$poverlapmethod
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($input_files_itables)
19 #end if 23 #end if
20 24
25 --o-merged-table=omergedtable
21 26
22 #if str($poverlapmethod) != 'None': 27 #if str($examples) != 'None':
23 --p-overlap-method=$poverlapmethod 28 --examples=$examples
24 #end if 29 #end if
25 30
26
27 --o-merged-table=omergedtable
28 ; 31 ;
29 cp omergedtable.qza $omergedtable 32 cp omergedtable.qza $omergedtable
30 ]]></command>
31 <inputs>
32 <repeat name="input_files_itables" optional="False" title="--i-tables">
33 <param format="qza,no_unzip.zip" label="--i-tables: PATH List[FeatureTable[Frequency]] The collection of feature tables to be merged. [required]" name="additional_input" type="data"/>
34 </repeat>
35 33
36 <param label="--p-overlap-method: " name="poverlapmethod" optional="True" type="select"> 34 ]]></command>
37 <option selected="True" value="None">Selection is Optional</option> 35 <inputs>
38 <option value="error_on_overlapping_sample">error_on_overlapping_sample</option> 36 <repeat name="input_files_itables" optional="False" title="--i-tables">
39 <option value="error_on_overlapping_feature">error_on_overlapping_feature</option> 37 <param format="qza,no_unzip.zip" label="--i-tables: ARTIFACTS... List[FeatureTable[Frequency]] The collection of feature tables to be merged. [required]" name="additional_input" optional="False" type="data" />
40 <option value="sum">sum</option> 38 </repeat>
41 </param> 39 <param label="--p-overlap-method: " name="poverlapmethod" optional="True" type="select">
42 </inputs> 40 <option selected="True" value="None">Selection is Optional</option>
43 <outputs> 41 <option value="error_on_overlapping_sample">error_on_overlapping_sample</option>
44 <data format="qza" label="${tool.name} on ${on_string}: mergedtable.qza" name="omergedtable"/> 42 <option value="error_on_overlapping_feature">error_on_overlapping_feature</option>
45 </outputs> 43 <option value="sum">sum</option>
46 <help><![CDATA[ 44 </param>
45 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
46
47 </inputs>
48
49 <outputs>
50 <data format="qza" label="${tool.name} on ${on_string}: mergedtable.qza" name="omergedtable" />
51
52 </outputs>
53
54 <help><![CDATA[
47 Combine multiple tables 55 Combine multiple tables
48 ####################### 56 ###############################################################
49 57
50 Combines feature tables using the `overlap_method` provided. 58 Combines feature tables using the `overlap_method` provided.
51 59
52 Parameters 60 Parameters
53 ---------- 61 ----------
58 66
59 Returns 67 Returns
60 ------- 68 -------
61 merged_table : FeatureTable[Frequency] 69 merged_table : FeatureTable[Frequency]
62 The resulting merged feature table. 70 The resulting merged feature table.
63 ]]></help> 71 ]]></help>
64 <macros> 72 <macros>
65 <import>qiime_citation.xml</import> 73 <import>qiime_citation.xml</import>
66 </macros> 74 </macros>
67 <expand macro="qiime_citation"/> 75 <expand macro="qiime_citation"/>
68 </tool> 76 </tool>