Mercurial > repos > florianbegusch > qiime2_all
diff qiime_composition_ancom.xml @ 0:09b7bcb72fa7 draft
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author | florianbegusch |
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date | Thu, 24 May 2018 02:11:44 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime_composition_ancom.xml Thu May 24 02:11:44 2018 -0400 @@ -0,0 +1,90 @@ +<?xml version="1.0" ?> +<tool id="qiime_composition_ancom" name="qiime composition ancom" version="2018.4"> + <description> - Apply ANCOM to identify features that differ in abundance.</description> + <requirements> + <requirement type="package" version="2018.4">qiime2</requirement> + </requirements> + <command><![CDATA[ + + qiime composition ancom --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($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn" + + #if str($pdifferencefunction) != 'None': + --p-difference-function=$pdifferencefunction + #end if + + #if str($cmdconfig) != 'None': + --cmd-config=$cmdconfig + #end if + + #if str($ptransformfunction) != 'None': + --p-transform-function=$ptransformfunction + #end if + + --o-visualization=ovisualization; + + qiime tools export ovisualization.qzv --output-dir 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: FeatureTable[Composition] - The feature table to be used for ANCOM computation. [required]" name="itable" optional="False" type="data"/> + <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> + <param format="tabular" label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data"/> + </repeat> + <param label="--m-metadata-column: MetadataColumn[Categorical] - Column from metadata file or artifact viewable as metadata. The categorical sample metadata column to test for differential abundance across. [required]" name="mmetadatacolumn" optional="False" type="text"/> + <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="mean_difference">mean_difference</option> + <option value="f_statistic">f_statistic</option> + </param> + <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/> + <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="log">log</option> + <option value="clr">clr</option> + <option value="sqrt">sqrt</option> + </param> + </inputs> + <outputs> + <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> + </outputs> + <help> +<![CDATA[ +Apply ANCOM to identify features that differ in abundance. +---------------------------------------------------------- + +Apply Analysis of Composition of Microbiomes (ANCOM) to identify features +that are differentially abundant across groups. + +Parameters +---------- +table : FeatureTable[Composition] + The feature table to be used for ANCOM computation. +metadata : MetadataColumn[Categorical] + The categorical sample metadata column to test for differential + abundance across. +transform_function : Str % Choices({'clr', 'log', 'sqrt'}), optional + The method applied to transform feature values before generating + volcano plots. +difference_function : Str % Choices({'f_statistic', 'mean_difference'}), optional + The method applied to visualize fold difference in feature abundances + across groups for volcano plots. + +Returns +------- +visualization : Visualization + +]]> +</help> +</tool>