Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_demux_emp-single.xml @ 14:a0a8d77a991c draft
Uploaded
author | florianbegusch |
---|---|
date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
children |
line wrap: on
line diff
--- a/qiime2/qiime_demux_emp-single.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_demux_emp-single.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,26 +1,47 @@ <?xml version="1.0" ?> -<tool id="qiime_demux_emp-single" name="qiime demux emp-single" version="2019.7"> - <description> - Demultiplex sequence data generated with the EMP protocol.</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<tool id="qiime_demux_emp-single" name="qiime demux emp-single" + version="2020.8"> + <description>Demultiplex sequence data generated with the EMP protocol.</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ qiime demux emp-single --i-seqs=$iseqs ---m-barcodes-column="$mbarcodescolumn" - +# if $input_files_mbarcodesfile: + # def list_dict_to_string(list_dict): + # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') + # for d in list_dict[1:]: + # set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name') + # end for + # return $file_list + # end def +--m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) +# end if -#if $input_files_mbarcodesfile: -#def list_dict_to_string(list_dict): -#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') -#for d in list_dict[1:]: - #set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name') -#end for -#return $file_list -#end def ---m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) +#if '__ob__' in str($mbarcodescolumn): + #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[') + #set $mbarcodescolumn = $mbarcodescolumn_temp +#end if +#if '__cb__' in str($mbarcodescolumn): + #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']') + #set $mbarcodescolumn = $mbarcodescolumn_temp #end if +#if 'X' in str($mbarcodescolumn): + #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\') + #set $mbarcodescolumn = $mbarcodescolumn_temp +#end if +#if '__sq__' in str($mbarcodescolumn): + #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'") + #set $mbarcodescolumn = $mbarcodescolumn_temp +#end if +#if '__db__' in str($mbarcodescolumn): + #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"') + #set $mbarcodescolumn = $mbarcodescolumn_temp +#end if + +--m-barcodes-column=$mbarcodescolumn #if $pnogolayerrorcorrection: @@ -36,29 +57,39 @@ #end if --o-per-sample-sequences=opersamplesequences + --o-error-correction-details=oerrorcorrectiondetails + +#if str($examples) != 'None': +--examples=$examples +#end if + ; -cp opersamplesequences.qza $opersamplesequences; cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails - ]]></command> - <inputs> - <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file [optional]"> - <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip"/> - </repeat> - <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT RawSequences | EMPSingleEndSequences | EMPPairedEndSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/> - <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/> - <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: False]" name="pnogolayerrorcorrection" selected="False" type="boolean"/> - <param label="--p-rev-comp-barcodes: --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean"/> - <param label="--p-rev-comp-mapping-barcodes: --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean"/> - </inputs> - <outputs> - <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/> - <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails"/> - </outputs> - <help><![CDATA[ + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT RawSequences | EMPSingleEndSequences | EMPPairedEndSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" /> + <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file"> + <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" /> + </repeat> + <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text" /> + <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: True]" name="pnogolayerrorcorrection" selected="False" type="boolean" /> + <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-barcodes: --p-rev-comp-barcodes: / --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean" /> + <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-mapping-barcodes: --p-rev-comp-mapping-barcodes: / --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" /> + <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails" /> + + </outputs> + + <help><![CDATA[ Demultiplex sequence data generated with the EMP protocol. -########################################################## +############################################################### Demultiplex sequence data (i.e., map barcode reads to sample ids) for data generated with the Earth Microbiome Project (EMP) amplicon sequencing @@ -86,9 +117,9 @@ The resulting demultiplexed sequences. error_correction_details : ErrorCorrectionDetails Detail about the barcode error corrections. - ]]></help> -<macros> + ]]></help> + <macros> <import>qiime_citation.xml</import> -</macros> -<expand macro="qiime_citation"/> -</tool> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file