Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_longitudinal_plot-feature-volatility.xml @ 0:370e0b6e9826 draft
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| author | florianbegusch |
|---|---|
| date | Wed, 17 Jul 2019 03:05:17 -0400 |
| parents | |
| children | 914fa4daf16a |
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| -1:000000000000 | 0:370e0b6e9826 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_longitudinal_plot-feature-volatility" name="qiime longitudinal plot-feature-volatility" version="2019.4"> | |
| 3 <description> - Plot longitudinal feature volatility and importances</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2019.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command><![CDATA[ | |
| 8 qiime longitudinal plot-feature-volatility | |
| 9 | |
| 10 --i-table=$itable | |
| 11 --i-importances=$iimportances | |
| 12 --p-state-column="$pstatecolumn" | |
| 13 | |
| 14 #if str($pindividualidcolumn): | |
| 15 --p-individual-id-column="$pindividualidcolumn" | |
| 16 #end if | |
| 17 | |
| 18 #if str($pdefaultgroupcolumn): | |
| 19 --p-default-group-column="$pdefaultgroupcolumn" | |
| 20 #end if | |
| 21 | |
| 22 #if str($pyscale) != 'None': | |
| 23 --p-yscale=$pyscale | |
| 24 #end if | |
| 25 | |
| 26 | |
| 27 #if $input_files_mmetadatafile: | |
| 28 #def list_dict_to_string(list_dict): | |
| 29 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') | |
| 30 #for d in list_dict[1:]: | |
| 31 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') | |
| 32 #end for | |
| 33 #return $file_list | |
| 34 #end def | |
| 35 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) | |
| 36 #end if | |
| 37 | |
| 38 | |
| 39 --o-visualization=ovisualization | |
| 40 ; | |
| 41 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' | |
| 42 && cp -r out/* '$ovisualization.files_path' | |
| 43 && mv '$ovisualization.files_path/index.html' '$ovisualization' | |
| 44 ]]></command> | |
| 45 <inputs> | |
| 46 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing features found in importances. [required]" name="itable" optional="False" type="data"/> | |
| 47 <param format="qza,no_unzip.zip" label="--i-importances: ARTIFACT FeatureData[Importance] Feature importance scores. [required]" name="iimportances" optional="False" type="data"/> | |
| 48 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/> | |
| 49 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [optional]" name="pindividualidcolumn" optional="True" type="text"/> | |
| 50 <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="True" type="text"/> | |
| 51 <param label="--p-yscale: " name="pyscale" optional="True" type="select"> | |
| 52 <option selected="True" value="None">Selection is Optional</option> | |
| 53 <option value="linear">linear</option> | |
| 54 <option value="pow">pow</option> | |
| 55 <option value="sqrt">sqrt</option> | |
| 56 <option value="log">log</option> | |
| 57 </param> | |
| 58 | |
| 59 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> | |
| 60 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> | |
| 61 </repeat> | |
| 62 | |
| 63 </inputs> | |
| 64 <outputs> | |
| 65 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> | |
| 66 </outputs> | |
| 67 <help><![CDATA[ | |
| 68 Plot longitudinal feature volatility and importances | |
| 69 #################################################### | |
| 70 | |
| 71 Plots an interactive control chart of feature abundances (y-axis) in each | |
| 72 sample across time (or state; x-axis). Feature importance scores and | |
| 73 descriptive statistics for each each feature are plotted in interactive bar | |
| 74 charts below the control chart, facilitating exploration of longitudinal | |
| 75 feature data. This visualization is intended for use with the feature- | |
| 76 volatility pipeline; use that pipeline to access this visualization. | |
| 77 | |
| 78 Parameters | |
| 79 ---------- | |
| 80 table : FeatureTable[RelativeFrequency] | |
| 81 Feature table containing features found in importances. | |
| 82 importances : FeatureData[Importance] | |
| 83 Feature importance scores. | |
| 84 metadata : Metadata | |
| 85 Sample metadata file containing individual_id_column. | |
| 86 state_column : Str | |
| 87 Metadata column containing state (time) variable information. | |
| 88 individual_id_column : Str, optional | |
| 89 Metadata column containing IDs for individual subjects. | |
| 90 default_group_column : Str, optional | |
| 91 The default metadata column on which to separate groups for comparison | |
| 92 (all categorical metadata columns will be available in the | |
| 93 visualization). | |
| 94 yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional | |
| 95 y-axis scaling strategy to apply. | |
| 96 | |
| 97 Returns | |
| 98 ------- | |
| 99 visualization : Visualization | |
| 100 ]]></help> | |
| 101 <macros> | |
| 102 <import>qiime_citation.xml</import> | |
| 103 </macros> | |
| 104 <expand macro="qiime_citation"/> | |
| 105 </tool> |