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comparison qiime2/qiime_cutadapt_demux-single.xml @ 4:914fa4daf16a draft

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Fixes
author florianbegusch
date Wed, 31 Jul 2019 03:06:00 -0400
parents 51025741f326
children f190567fe3f6
comparison
equal deleted inserted replaced
3:558645416841 4:914fa4daf16a
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime cutadapt demux-single 8 qiime cutadapt demux-single
9 9
10 --i-seqs=$iseqs 10 --i-seqs=$iseqs
11
12
13
14 #if '__sq__' in str($mbarcodescolumn):
15 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
16 #set $mbarcodescolumn = $mbarcodescolumn_temp
17 #end if
18
11 --m-barcodes-column="$mbarcodescolumn" 19 --m-barcodes-column="$mbarcodescolumn"
20
21
12 --o-per-sample-sequences=opersamplesequences 22 --o-per-sample-sequences=opersamplesequences
13 --o-untrimmed-sequences=ountrimmedsequences 23 --o-untrimmed-sequences=ountrimmedsequences
14 24
15 25
26
27
28
29
16 #if $input_files_mbarcodesfile: 30 #if $input_files_mbarcodesfile:
17 #def list_dict_to_string(list_dict): 31 #def list_dict_to_string(list_dict):
18 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 32 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
19 #for d in list_dict[1:]: 33 #for d in list_dict[1:]:
20 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 34 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
21 #end for 35 #end for
22 #return $file_list 36 #return $file_list
23 #end def 37 #end def
24 --m-barcodes-file=$list_dict_to_string("$input_files_mbarcodesfile") 38 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
25 #end if 39 #end if
40
26 41
27 #if $perrorrate: 42 #if $perrorrate:
28 --p-error-rate=$perrorrate 43 --p-error-rate=$perrorrate
29 #end if 44 #end if
30 45
33 cp opersamplesequences.qza $opersamplesequences; 48 cp opersamplesequences.qza $opersamplesequences;
34 cp ountrimmedsequences.qza $ountrimmedsequences 49 cp ountrimmedsequences.qza $ountrimmedsequences
35 ]]></command> 50 ]]></command>
36 <inputs> 51 <inputs>
37 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/> 52 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
38 <repeat name="$input_files_mbarcodesfile" optional="False" title="--m-barcodes-file"> 53 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
39 <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 54 <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
40 </repeat> 55 </repeat>
41 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/> 56 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>
42 <param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%). [default: 0.1]" name="perrorrate" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.1"/> 57 <param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%). [default: 0.1]" name="perrorrate" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.1"/>
43 </inputs> 58 </inputs>