Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_demux_emp-single.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_emp-single" name="qiime demux emp-single" version="2019.7"> | 2 <tool id="qiime_demux_emp-single" name="qiime demux emp-single" |
3 <description> - Demultiplex sequence data generated with the EMP protocol.</description> | 3 version="2020.8"> |
4 <requirements> | 4 <description>Demultiplex sequence data generated with the EMP protocol.</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 demux emp-single | 9 qiime demux emp-single |
9 | 10 |
10 --i-seqs=$iseqs | 11 --i-seqs=$iseqs |
11 --m-barcodes-column="$mbarcodescolumn" | 12 # if $input_files_mbarcodesfile: |
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-barcodes-file=' + d['additional_input'].__getattr__('file_name') | |
17 # end for | |
18 # return $file_list | |
19 # end def | |
20 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) | |
21 # end if | |
12 | 22 |
23 #if '__ob__' in str($mbarcodescolumn): | |
24 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[') | |
25 #set $mbarcodescolumn = $mbarcodescolumn_temp | |
26 #end if | |
27 #if '__cb__' in str($mbarcodescolumn): | |
28 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']') | |
29 #set $mbarcodescolumn = $mbarcodescolumn_temp | |
30 #end if | |
31 #if 'X' in str($mbarcodescolumn): | |
32 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\') | |
33 #set $mbarcodescolumn = $mbarcodescolumn_temp | |
34 #end if | |
35 #if '__sq__' in str($mbarcodescolumn): | |
36 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'") | |
37 #set $mbarcodescolumn = $mbarcodescolumn_temp | |
38 #end if | |
39 #if '__db__' in str($mbarcodescolumn): | |
40 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"') | |
41 #set $mbarcodescolumn = $mbarcodescolumn_temp | |
42 #end if | |
13 | 43 |
14 #if $input_files_mbarcodesfile: | 44 --m-barcodes-column=$mbarcodescolumn |
15 #def list_dict_to_string(list_dict): | |
16 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') | |
17 #for d in list_dict[1:]: | |
18 #set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name') | |
19 #end for | |
20 #return $file_list | |
21 #end def | |
22 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) | |
23 #end if | |
24 | 45 |
25 | 46 |
26 #if $pnogolayerrorcorrection: | 47 #if $pnogolayerrorcorrection: |
27 --p-no-golay-error-correction | 48 --p-no-golay-error-correction |
28 #end if | 49 #end if |
34 #if $prevcompmappingbarcodes: | 55 #if $prevcompmappingbarcodes: |
35 --p-rev-comp-mapping-barcodes | 56 --p-rev-comp-mapping-barcodes |
36 #end if | 57 #end if |
37 | 58 |
38 --o-per-sample-sequences=opersamplesequences | 59 --o-per-sample-sequences=opersamplesequences |
60 | |
39 --o-error-correction-details=oerrorcorrectiondetails | 61 --o-error-correction-details=oerrorcorrectiondetails |
62 | |
63 #if str($examples) != 'None': | |
64 --examples=$examples | |
65 #end if | |
66 | |
40 ; | 67 ; |
41 cp opersamplesequences.qza $opersamplesequences; | |
42 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails | 68 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails |
43 ]]></command> | |
44 <inputs> | |
45 <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file [optional]"> | |
46 <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip"/> | |
47 </repeat> | |
48 | 69 |
49 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT RawSequences | EMPSingleEndSequences | EMPPairedEndSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/> | 70 ]]></command> |
50 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/> | 71 <inputs> |
51 <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: False]" name="pnogolayerrorcorrection" selected="False" type="boolean"/> | 72 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT RawSequences | EMPSingleEndSequences | EMPPairedEndSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" /> |
52 <param label="--p-rev-comp-barcodes: --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean"/> | 73 <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file"> |
53 <param label="--p-rev-comp-mapping-barcodes: --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean"/> | 74 <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" /> |
54 </inputs> | 75 </repeat> |
55 <outputs> | 76 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text" /> |
56 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/> | 77 <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: True]" name="pnogolayerrorcorrection" selected="False" type="boolean" /> |
57 <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails"/> | 78 <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-barcodes: --p-rev-comp-barcodes: / --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean" /> |
58 </outputs> | 79 <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-mapping-barcodes: --p-rev-comp-mapping-barcodes: / --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean" /> |
59 <help><![CDATA[ | 80 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> |
81 | |
82 </inputs> | |
83 | |
84 <outputs> | |
85 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" /> | |
86 <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails" /> | |
87 | |
88 </outputs> | |
89 | |
90 <help><![CDATA[ | |
60 Demultiplex sequence data generated with the EMP protocol. | 91 Demultiplex sequence data generated with the EMP protocol. |
61 ########################################################## | 92 ############################################################### |
62 | 93 |
63 Demultiplex sequence data (i.e., map barcode reads to sample ids) for data | 94 Demultiplex sequence data (i.e., map barcode reads to sample ids) for data |
64 generated with the Earth Microbiome Project (EMP) amplicon sequencing | 95 generated with the Earth Microbiome Project (EMP) amplicon sequencing |
65 protocol. Details about this protocol can be found at | 96 protocol. Details about this protocol can be found at |
66 http://www.earthmicrobiome.org/protocols-and-standards/ | 97 http://www.earthmicrobiome.org/protocols-and-standards/ |
84 ------- | 115 ------- |
85 per_sample_sequences : SampleData[SequencesWithQuality] | 116 per_sample_sequences : SampleData[SequencesWithQuality] |
86 The resulting demultiplexed sequences. | 117 The resulting demultiplexed sequences. |
87 error_correction_details : ErrorCorrectionDetails | 118 error_correction_details : ErrorCorrectionDetails |
88 Detail about the barcode error corrections. | 119 Detail about the barcode error corrections. |
89 ]]></help> | 120 ]]></help> |
90 <macros> | 121 <macros> |
91 <import>qiime_citation.xml</import> | 122 <import>qiime_citation.xml</import> |
92 </macros> | 123 </macros> |
93 <expand macro="qiime_citation"/> | 124 <expand macro="qiime_citation"/> |
94 </tool> | 125 </tool> |