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author | florianbegusch |
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date | Thu, 24 May 2018 03:40:50 -0400 |
parents | 09b7bcb72fa7 |
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<?xml version="1.0" ?> <tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit" version="2018.4"> <description> - Nonparametric microbial interdependence test</description> <requirements> <requirement type="package" version="2018.4">qiime2</requirement> </requirements> <command> <![CDATA[ qiime longitudinal nmit --i-table=$itable #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 + ',' + d['additional_input'].__getattr__('file_name') #end for #return $file_list #end def --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-individual-id-column="$pindividualidcolumn" #if str($cmdconfig) != 'None': --cmd-config=$cmdconfig #end if #if str($pdistmethod) != 'None': --p-dist-method=$pdistmethod #end if #if str($pcorrmethod) != 'None': --p-corr-method=$pcorrmethod #end if --o-distance-matrix=odistancematrix; cp odistancematrix.qza $odistancematrix; ]]> </command> <inputs> <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[RelativeFrequency] Feature table to use for microbial interdependence test. [required]" name="itable" optional="False" type="data"/> <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> </repeat> <param label="--p-individual-id-column: Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/> <param label="--p-corr-method: The temporal correlation test to be applied. [default: kendall]" name="pcorrmethod" optional="True" type="select"> <option selected="True" value="None">Selection is Optional</option> <option value="kendall">kendall</option> <option value="pearson">pearson</option> <option value="spearman">spearman</option> </param> <param label="--p-dist-method: Temporal distance method, see numpy.linalg.norm for details. [default: fro]" name="pdistmethod" optional="True" type="select"> <option selected="True" value="None">Selection is Optional</option> <option value="fro">fro</option> <option value="nuc">nuc</option> </param> <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/> </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: distance-matrix.qza" name="odistancematrix"/> </outputs> <help> <![CDATA[ Nonparametric microbial interdependence test --------------------------------------------- Perform nonparametric microbial interdependence test to determine longitudinal sample similarity as a function of temporal microbial composition. For more details and citation, please see doi.org/10.1002/gepi.22065 Parameters ---------- table : FeatureTable[RelativeFrequency] Feature table to use for microbial interdependence test. metadata : Metadata Sample metadata file containing individual_id_column. individual_id_column : Str Metadata column containing IDs for individual subjects. corr_method : Str % Choices({'kendall', 'pearson', 'spearman'}), optional The temporal correlation test to be applied. dist_method : Str % Choices({'fro', 'nuc'}), optional Temporal distance method, see numpy.linalg.norm for details. Returns ------- distance_matrix : DistanceMatrix The resulting distance matrix. ]]> </help> </tool>