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comparison qiime2/qiime_demux_filter-samples.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
1 <?xml version="1.0" ?>
2 <tool id="qiime_demux_filter-samples" name="qiime demux filter-samples"
3 version="2020.8">
4 <description>Filter samples out of demultiplexed data.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime demux filter-samples
10
11 --i-demux=$idemux
12 # if $input_files_mmetadatafile:
13 # def list_dict_to_string(list_dict):
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 # for d in list_dict[1:]:
16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
21 # end if
22
23 #if '__ob__' in str($pwhere):
24 #set $pwhere_temp = $pwhere.replace('__ob__', '[')
25 #set $pwhere = $pwhere_temp
26 #end if
27 #if '__cb__' in str($pwhere):
28 #set $pwhere_temp = $pwhere.replace('__cb__', ']')
29 #set $pwhere = $pwhere_temp
30 #end if
31 #if 'X' in str($pwhere):
32 #set $pwhere_temp = $pwhere.replace('X', '\\')
33 #set $pwhere = $pwhere_temp
34 #end if
35 #if '__sq__' in str($pwhere):
36 #set $pwhere_temp = $pwhere.replace('__sq__', "'")
37 #set $pwhere = $pwhere_temp
38 #end if
39 #if '__db__' in str($pwhere):
40 #set $pwhere_temp = $pwhere.replace('__db__', '"')
41 #set $pwhere = $pwhere_temp
42 #end if
43
44 #if str($pwhere):
45 --p-where=$pwhere
46 #end if
47
48 #if $pexcludeids:
49 --p-exclude-ids
50 #end if
51
52 --o-filtered-demux=ofiltereddemux
53
54 #if str($examples) != 'None':
55 --examples=$examples
56 #end if
57
58 ;
59 cp ofiltereddemux.qza $ofiltereddemux
60
61 ]]></command>
62 <inputs>
63 <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] The demultiplexed data from which samples should be filtered. [required]" name="idemux" optional="False" type="data" />
64 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
65 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata indicating which sample ids to filter. arguments will The optional `where` parameter may be used to filter be merged) ids based on specified conditions in the metadata. The optional `exclude-ids` parameter may be used to exclude the ids specified in the metadata from the filter. [required]" name="additional_input" optional="False" type="data" />
66 </repeat>
67 <param label="--p-where: TEXT Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained. [optional]" name="pwhere" optional="False" type="text" />
68 <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]" name="pexcludeids" selected="False" type="boolean" />
69 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
70
71 </inputs>
72
73 <outputs>
74 <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux" />
75
76 </outputs>
77
78 <help><![CDATA[
79 Filter samples out of demultiplexed data.
80 ###############################################################
81
82 Filter samples indicated in given metadata out of demultiplexed data.
83 Specific samples can be further selected with the WHERE clause, and the
84 `exclude_ids` parameter allows for filtering of all samples not specified.
85
86 Parameters
87 ----------
88 demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
89 The demultiplexed data from which samples should be filtered.
90 metadata : Metadata
91 Sample metadata indicating which sample ids to filter. The optional
92 `where` parameter may be used to filter ids based on specified
93 conditions in the metadata. The optional `exclude_ids` parameter may be
94 used to exclude the ids specified in the metadata from the filter.
95 where : Str, optional
96 Optional SQLite WHERE clause specifying sample metadata criteria that
97 must be met to be included in the filtered data. If not provided, all
98 samples in `metadata` that are also in the demultiplexed data will be
99 retained.
100 exclude_ids : Bool, optional
101 Defaults to False. If True, the samples selected by the `metadata` and
102 optional `where` parameter will be excluded from the filtered data.
103
104 Returns
105 -------
106 filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
107 Filtered demultiplexed data.
108 ]]></help>
109 <macros>
110 <import>qiime_citation.xml</import>
111 </macros>
112 <expand macro="qiime_citation"/>
113 </tool>