Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_longitudinal_plot-feature-volatility.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_longitudinal_plot-feature-volatility.xml Fri Sep 04 13:12:49 2020 +0000 @@ -0,0 +1,235 @@ +<?xml version="1.0" ?> +<tool id="qiime_longitudinal_plot-feature-volatility" name="qiime longitudinal plot-feature-volatility" + version="2020.8"> + <description>Plot longitudinal feature volatility and importances</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime longitudinal plot-feature-volatility + +--i-table=$itable + +--i-importances=$iimportances +# 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($input_files_mmetadatafile) +# end if + +#if '__ob__' in str($pstatecolumn): + #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[') + #set $pstatecolumn = $pstatecolumn_temp +#end if +#if '__cb__' in str($pstatecolumn): + #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']') + #set $pstatecolumn = $pstatecolumn_temp +#end if +#if 'X' in str($pstatecolumn): + #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\') + #set $pstatecolumn = $pstatecolumn_temp +#end if +#if '__sq__' in str($pstatecolumn): + #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'") + #set $pstatecolumn = $pstatecolumn_temp +#end if +#if '__db__' in str($pstatecolumn): + #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"') + #set $pstatecolumn = $pstatecolumn_temp +#end if + +--p-state-column=$pstatecolumn + + +#if '__ob__' in str($pindividualidcolumn): + #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[') + #set $pindividualidcolumn = $pindividualidcolumn_temp +#end if +#if '__cb__' in str($pindividualidcolumn): + #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']') + #set $pindividualidcolumn = $pindividualidcolumn_temp +#end if +#if 'X' in str($pindividualidcolumn): + #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\') + #set $pindividualidcolumn = $pindividualidcolumn_temp +#end if +#if '__sq__' in str($pindividualidcolumn): + #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'") + #set $pindividualidcolumn = $pindividualidcolumn_temp +#end if +#if '__db__' in str($pindividualidcolumn): + #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"') + #set $pindividualidcolumn = $pindividualidcolumn_temp +#end if + +#if str($pindividualidcolumn): + --p-individual-id-column=$pindividualidcolumn +#end if + +#if '__ob__' in str($pdefaultgroupcolumn): + #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__ob__', '[') + #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp +#end if +#if '__cb__' in str($pdefaultgroupcolumn): + #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__cb__', ']') + #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp +#end if +#if 'X' in str($pdefaultgroupcolumn): + #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('X', '\\') + #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp +#end if +#if '__sq__' in str($pdefaultgroupcolumn): + #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__sq__', "'") + #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp +#end if +#if '__db__' in str($pdefaultgroupcolumn): + #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__db__', '"') + #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp +#end if + +#if str($pdefaultgroupcolumn): + --p-default-group-column=$pdefaultgroupcolumn +#end if + +#if str($pyscale) != 'None': +--p-yscale=$pyscale +#end if + +#if str($pimportancethreshold) != 'None': +--p-importance-threshold=$pimportancethreshold +#end if + +#if str($pfeaturecount) != 'None': +--p-feature-count=$pfeaturecount +#end if + +#if str($pmissingsamples) != 'None': +--p-missing-samples=$pmissingsamples +#end if + +--o-visualization=ovisualization + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp odistancematrix.qza $odistancematrix + +; +qiime tools export ovisualization.qzv --output-path out +&& mkdir -p '$ovisualization.files_path' +&& cp -r out/* '$ovisualization.files_path' +&& mv '$ovisualization.files_path/index.html' '$ovisualization' + +; +qiime tools export ovisualization.qzv --output-path out +&& mkdir -p '$ovisualization.files_path' +&& cp -r out/* '$ovisualization.files_path' +&& mv '$ovisualization.files_path/index.html' '$ovisualization' + +; +qiime tools export ovisualization.qzv --output-path out +&& mkdir -p '$ovisualization.files_path' +&& cp -r out/* '$ovisualization.files_path' +&& mv '$ovisualization.files_path/index.html' '$ovisualization' + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing features found in importances. [required]" name="itable" optional="False" type="data" /> + <param format="qza,no_unzip.zip" label="--i-importances: ARTIFACT FeatureData[Importance] Feature importance scores. [required]" name="iimportances" 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 file containing arguments will be individual-id-column. merged) [required]" name="additional_input" optional="False" type="data" /> + </repeat> + <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" /> + <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [optional]" name="pindividualidcolumn" optional="False" type="text" /> + <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="False" type="text" /> + <param label="--p-yscale: " name="pyscale" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="linear">linear</option> + <option value="pow">pow</option> + <option value="sqrt">sqrt</option> + <option value="log">log</option> + </param> + <param label="--p-importance-threshold: " name="pimportancethreshold" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="Float % Range(0">Float % Range(0</option> + <option value="None">None</option> + <option value="inclusive_start=False">inclusive_start=False</option> + </param> + <param label="--p-feature-count: " name="pfeaturecount" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="Int % Range(1">Int % Range(1</option> + <option value="None">None</option> + </param> + <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="error">error</option> + <option value="ignore">ignore</option> + </param> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" /> + + </outputs> + + <help><![CDATA[ +Plot longitudinal feature volatility and importances +############################################################### + +Plots an interactive control chart of feature abundances (y-axis) in each +sample across time (or state; x-axis). Feature importance scores and +descriptive statistics for each feature are plotted in interactive bar +charts below the control chart, facilitating exploration of longitudinal +feature data. This visualization is intended for use with the feature- +volatility pipeline; use that pipeline to access this visualization. + +Parameters +---------- +table : FeatureTable[RelativeFrequency] + Feature table containing features found in importances. +importances : FeatureData[Importance] + Feature importance scores. +metadata : Metadata + Sample metadata file containing individual_id_column. +state_column : Str + Metadata column containing state (time) variable information. +individual_id_column : Str, optional + Metadata column containing IDs for individual subjects. +default_group_column : Str, optional + The default metadata column on which to separate groups for comparison + (all categorical metadata columns will be available in the + visualization). +yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional + y-axis scaling strategy to apply. +importance_threshold : Float % Range(0, None, inclusive_start=False) | Str % Choices('q1', 'q2', 'q3'), optional + Filter feature table to exclude any features with an importance score + less than this threshold. Set to "q1", "q2", or "q3" to select the + first, second, or third quartile of values. Set to "None" to disable + this filter. +feature_count : Int % Range(1, None) | Str % Choices('all'), optional + Filter feature table to include top N most important features. Set to + "all" to include all features. +missing_samples : Str % Choices('error', 'ignore'), optional + How to handle missing samples in metadata. "error" will fail if missing + samples are detected. "ignore" will cause the feature table and + metadata to be filtered, so that only samples found in both files are + retained. + +Returns +------- +visualization : Visualization + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file