Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_feature-table_filter-seqs.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_feature-table_filter-seqs.xml Fri Sep 04 13:12:49 2020 +0000 @@ -0,0 +1,130 @@ +<?xml version="1.0" ?> +<tool id="qiime_feature-table_filter-seqs" name="qiime feature-table filter-seqs" + version="2020.8"> + <description>Filter features from sequences</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime feature-table filter-seqs +# if $input_files_idata: + # 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 + ' --i-data=' + d['additional_input'].__getattr__('file_name') + # end for + # return $file_list + # end def +--i-data=$list_dict_to_string($input_files_idata) +# end if + +#if str($itable) != 'None': +--i-table=$itable +#end if +# 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 $pexcludeids: + --p-exclude-ids +#end if + +--o-filtered-data=ofiltereddata + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp ofiltereddata.qza $ofiltereddata + + ]]></command> + <inputs> + <repeat name="input_files_idata" optional="False" title="--i-data"> + <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence¹ | AlignedSequence²] The sequences from which features should be filtered. [required]" name="additional_input" optional="False" type="data" /> + </repeat> + <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Table containing feature ids used for id-based filtering. [optional]" name="itable" optional="False" type="data" /> + <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> + <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Feature metadata used for id-based filtering, with arguments will `where` parameter when selecting features to retain, or be merged) with `exclude-ids` when selecting features to discard. [optional]" name="additional_input" optional="True" type="data" /> + </repeat> + <param label="--p-where: TEXT SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the sequences will be retained. [optional]" name="pwhere" optional="False" type="text" /> + <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids If true, the features selected by the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: filtereddata.qza" name="ofiltereddata" /> + + </outputs> + + <help><![CDATA[ +Filter features from sequences +############################################################### + +Filter features from sequences based on a feature table or metadata. See +the filtering tutorial on https://docs.qiime2.org for additional details. +This method can filter based on ids in a table or a metadata file, but not +both (i.e., the table and metadata options are mutually exclusive). + +Parameters +---------- +data : FeatureData[Sequence¹ | AlignedSequence²] + The sequences from which features should be filtered. +table : FeatureTable[Frequency], optional + Table containing feature ids used for id-based filtering. +metadata : Metadata, optional + Feature metadata used for id-based filtering, with `where` parameter + when selecting features to retain, or with `exclude_ids` when selecting + features to discard. +where : Str, optional + SQLite WHERE clause specifying feature metadata criteria that must be + met to be included in the filtered feature table. If not provided, all + features in `metadata` that are also in the sequences will be retained. +exclude_ids : Bool, optional + If true, the features selected by the `metadata` (with or without the + `where` parameter) or `table` parameter will be excluded from the + filtered sequences instead of being retained. + +Returns +------- +filtered_data : FeatureData[Sequence¹ | AlignedSequence²] + The resulting filtered sequences. + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file