Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_demux_filter-samples.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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13:887cd4ad8e16 | 14:a0a8d77a991c |
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1 <?xml version="1.0" ?> | 1 <?xml version="1.0" ?> |
2 <tool id="qiime_demux_filter-samples" name="qiime demux filter-samples" version="2019.7"> | 2 <tool id="qiime_demux_filter-samples" name="qiime demux filter-samples" |
3 <description> - Filter samples out of demultiplexed data.</description> | 3 version="2020.8"> |
4 <requirements> | 4 <description>Filter samples out of demultiplexed data.</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 qiime demux filter-samples | 8 <command><![CDATA[ |
9 | 9 qiime demux filter-samples |
10 | |
10 --i-demux=$idemux | 11 --i-demux=$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($input_files_mmetadatafile) | |
21 # end if | |
11 | 22 |
12 | 23 #if '__ob__' in str($pwhere): |
13 #if $input_files_mmetadatafile: | 24 #set $pwhere_temp = $pwhere.replace('__ob__', '[') |
14 #def list_dict_to_string(list_dict): | 25 #set $pwhere = $pwhere_temp |
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') | |
16 #for d in list_dict[1:]: | |
17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') | |
18 #end for | |
19 #return $file_list | |
20 #end def | |
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) | |
22 #end if | 26 #end if |
23 | 27 #if '__cb__' in str($pwhere): |
24 | 28 #set $pwhere_temp = $pwhere.replace('__cb__', ']') |
25 | 29 #set $pwhere = $pwhere_temp |
30 #end if | |
31 #if 'X' in str($pwhere): | |
32 #set $pwhere_temp = $pwhere.replace('X', '\\') | |
33 #set $pwhere = $pwhere_temp | |
34 #end if | |
26 #if '__sq__' in str($pwhere): | 35 #if '__sq__' in str($pwhere): |
27 #set $pwhere_temp = $pwhere.replace('__sq__', "'") | 36 #set $pwhere_temp = $pwhere.replace('__sq__', "'") |
28 #set $pwhere = $pwhere_temp | 37 #set $pwhere = $pwhere_temp |
29 #end if | 38 #end if |
30 | 39 #if '__db__' in str($pwhere): |
40 #set $pwhere_temp = $pwhere.replace('__db__', '"') | |
41 #set $pwhere = $pwhere_temp | |
42 #end if | |
31 | 43 |
32 #if str($pwhere): | 44 #if str($pwhere): |
33 --p-where="$pwhere" | 45 --p-where=$pwhere |
34 #end if | 46 #end if |
35 | |
36 | 47 |
37 #if $pexcludeids: | 48 #if $pexcludeids: |
38 --p-exclude-ids | 49 --p-exclude-ids |
39 #end if | 50 #end if |
40 | 51 |
52 --o-filtered-demux=ofiltereddemux | |
41 | 53 |
42 --o-filtered-demux=ofiltereddemux | 54 #if str($examples) != 'None': |
55 --examples=$examples | |
56 #end if | |
43 | 57 |
44 ; | 58 ; |
45 cp ofiltereddemux.qza $ofiltereddemux | 59 cp ofiltereddemux.qza $ofiltereddemux |
46 ]]></command> | |
47 <inputs> | |
48 | 60 |
49 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> | 61 ]]></command> |
50 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> | 62 <inputs> |
51 </repeat> | 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> | |
52 | 72 |
53 <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"/> | 73 <outputs> |
54 <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="True" type="text"/> | 74 <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux" /> |
55 <param label="--p-exclude-ids: --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]" name="pexcludeids" selected="False" type="boolean"/> | 75 |
56 </inputs> | 76 </outputs> |
57 <outputs> | 77 |
58 <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux"/> | 78 <help><![CDATA[ |
59 </outputs> | |
60 <help><![CDATA[ | |
61 Filter samples out of demultiplexed data. | 79 Filter samples out of demultiplexed data. |
62 ######################################### | 80 ############################################################### |
63 | 81 |
64 Filter samples indicated in given metadata out of demultiplexed data. | 82 Filter samples indicated in given metadata out of demultiplexed data. |
65 Specific samples can be further selected with the WHERE clause, and the | 83 Specific samples can be further selected with the WHERE clause, and the |
66 `exclude_ids` parameter allows for filtering of all samples not specified. | 84 `exclude_ids` parameter allows for filtering of all samples not specified. |
67 | 85 |
85 | 103 |
86 Returns | 104 Returns |
87 ------- | 105 ------- |
88 filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] | 106 filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] |
89 Filtered demultiplexed data. | 107 Filtered demultiplexed data. |
90 ]]></help> | 108 ]]></help> |
91 <macros> | 109 <macros> |
92 <import>qiime_citation.xml</import> | 110 <import>qiime_citation.xml</import> |
93 </macros> | 111 </macros> |
94 <expand macro="qiime_citation"/> | 112 <expand macro="qiime_citation"/> |
95 </tool> | 113 </tool> |