Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_demux_filter-samples.xml @ 29:3ba9833030c1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 13:12:49 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_demux_filter-samples.xml Fri Sep 04 13:12:49 2020 +0000 @@ -0,0 +1,113 @@ +<?xml version="1.0" ?> +<tool id="qiime_demux_filter-samples" name="qiime demux filter-samples" + version="2020.8"> + <description>Filter samples out of demultiplexed data.</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime demux filter-samples + +--i-demux=$idemux +# if $input_files_mmetadatafile: + # 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-metadata-file=' + d['additional_input'].__getattr__('file_name') + # end for + # return $file_list + # end def +--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) +# end if + +#if '__ob__' in str($pwhere): + #set $pwhere_temp = $pwhere.replace('__ob__', '[') + #set $pwhere = $pwhere_temp +#end if +#if '__cb__' in str($pwhere): + #set $pwhere_temp = $pwhere.replace('__cb__', ']') + #set $pwhere = $pwhere_temp +#end if +#if 'X' in str($pwhere): + #set $pwhere_temp = $pwhere.replace('X', '\\') + #set $pwhere = $pwhere_temp +#end if +#if '__sq__' in str($pwhere): + #set $pwhere_temp = $pwhere.replace('__sq__', "'") + #set $pwhere = $pwhere_temp +#end if +#if '__db__' in str($pwhere): + #set $pwhere_temp = $pwhere.replace('__db__', '"') + #set $pwhere = $pwhere_temp +#end if + +#if str($pwhere): + --p-where=$pwhere +#end if + +#if $pexcludeids: + --p-exclude-ids +#end if + +--o-filtered-demux=ofiltereddemux + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp ofiltereddemux.qza $ofiltereddemux + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] The demultiplexed data from which samples should be filtered. [required]" name="idemux" optional="False" type="data" /> + <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> + <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata indicating which sample ids to filter. arguments will The optional `where` parameter may be used to filter be merged) ids based on specified conditions in the metadata. The optional `exclude-ids` parameter may be used to exclude the ids specified in the metadata from the filter. [required]" name="additional_input" optional="False" type="data" /> + </repeat> + <param label="--p-where: TEXT Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained. [optional]" name="pwhere" optional="False" type="text" /> + <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]" name="pexcludeids" selected="False" type="boolean" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux" /> + + </outputs> + + <help><![CDATA[ +Filter samples out of demultiplexed data. +############################################################### + +Filter samples indicated in given metadata out of demultiplexed data. +Specific samples can be further selected with the WHERE clause, and the +`exclude_ids` parameter allows for filtering of all samples not specified. + +Parameters +---------- +demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] + The demultiplexed data from which samples should be filtered. +metadata : Metadata + Sample metadata indicating which sample ids to filter. The optional + `where` parameter may be used to filter 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. +where : Str, optional + 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. +exclude_ids : Bool, optional + Defaults to False. If True, the samples selected by the `metadata` and + optional `where` parameter will be excluded from the filtered data. + +Returns +------- +filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] + Filtered demultiplexed data. + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file