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comparison qiime2/qiime_feature-table_merge-seqs.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-seqs" name="qiime feature-table merge-seqs" version="2019.7"> 2 <tool id="qiime_feature-table_merge-seqs" name="qiime feature-table merge-seqs"
3 <description> - Combine collections of feature sequences</description> 3 version="2020.8">
4 <requirements> 4 <description>Combine collections of feature sequences</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-seqs 9 qiime feature-table merge-seqs
10 # if $input_files_idata:
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-data=' + d['additional_input'].__getattr__('file_name')
15 # end for
16 # return $file_list
17 # end def
18 --i-data=$list_dict_to_string($input_files_idata)
19 # end if
9 20
21 --o-merged-data=omergeddata
10 22
11 #if $input_files_idata: 23 #if str($examples) != 'None':
12 #def list_dict_to_string(list_dict): 24 --examples=$examples
13 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
14 #for d in list_dict[1:]:
15 #set $file_list = $file_list + ' --i-data=' + d['additional_input'].__getattr__('file_name')
16 #end for
17 #return $file_list
18 #end def
19 --i-data=$list_dict_to_string($input_files_idata)
20 #end if 25 #end if
21 26
22
23 --o-merged-data=omergeddata
24 ; 27 ;
25 cp omergeddata.qza $omergeddata 28 cp omergeddata.qza $omergeddata
26 ]]></command>
27 <inputs>
28 <repeat name="input_files_idata" optional="False" title="--i-data">
29 <param format="qza,no_unzip.zip" label="--i-data: PATH List[FeatureData[Sequence]] The collection of feature sequences to be merged. [required]" name="additional_input" type="data"/>
30 </repeat>
31 29
32 </inputs> 30 ]]></command>
33 <outputs> 31 <inputs>
34 <data format="qza" label="${tool.name} on ${on_string}: mergeddata.qza" name="omergeddata"/> 32 <repeat name="input_files_idata" optional="False" title="--i-data">
35 </outputs> 33 <param format="qza,no_unzip.zip" label="--i-data: ARTIFACTS... List[FeatureData[Sequence]] The collection of feature sequences to be merged. [required]" name="additional_input" optional="False" type="data" />
36 <help><![CDATA[ 34 </repeat>
35 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
36
37 </inputs>
38
39 <outputs>
40 <data format="qza" label="${tool.name} on ${on_string}: mergeddata.qza" name="omergeddata" />
41
42 </outputs>
43
44 <help><![CDATA[
37 Combine collections of feature sequences 45 Combine collections of feature sequences
38 ######################################## 46 ###############################################################
39 47
40 Combines feature data objects which may or may not contain data for the 48 Combines feature data objects which may or may not contain data for the
41 same features. If different feature data is present for the same feature id 49 same features. If different feature data is present for the same feature id
42 in the inputs, the data from the first will be propagated to the result. 50 in the inputs, the data from the first will be propagated to the result.
43 51
49 Returns 57 Returns
50 ------- 58 -------
51 merged_data : FeatureData[Sequence] 59 merged_data : FeatureData[Sequence]
52 The resulting collection of feature sequences containing all feature 60 The resulting collection of feature sequences containing all feature
53 sequences provided. 61 sequences provided.
54 ]]></help> 62 ]]></help>
55 <macros> 63 <macros>
56 <import>qiime_citation.xml</import> 64 <import>qiime_citation.xml</import>
57 </macros> 65 </macros>
58 <expand macro="qiime_citation"/> 66 <expand macro="qiime_citation"/>
59 </tool> 67 </tool>