Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_diversity_beta-group-significance.xml @ 29:3ba9833030c1 draft
Uploaded
author | florianbegusch |
---|---|
date | Fri, 04 Sep 2020 13:12:49 +0000 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_beta-group-significance.xml Fri Sep 04 13:12:49 2020 +0000 @@ -0,0 +1,132 @@ +<?xml version="1.0" ?> +<tool id="qiime_diversity_beta-group-significance" name="qiime diversity beta-group-significance" + version="2020.8"> + <description>Beta diversity group significance</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime diversity beta-group-significance + +--i-distance-matrix=$idistancematrix +# 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($input_files_mmetadatafile) +# end if + +#if '__ob__' in str($mmetadatacolumn): + #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[') + #set $mmetadatacolumn = $mmetadatacolumn_temp +#end if +#if '__cb__' in str($mmetadatacolumn): + #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']') + #set $mmetadatacolumn = $mmetadatacolumn_temp +#end if +#if 'X' in str($mmetadatacolumn): + #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\') + #set $mmetadatacolumn = $mmetadatacolumn_temp +#end if +#if '__sq__' in str($mmetadatacolumn): + #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'") + #set $mmetadatacolumn = $mmetadatacolumn_temp +#end if +#if '__db__' in str($mmetadatacolumn): + #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"') + #set $mmetadatacolumn = $mmetadatacolumn_temp +#end if + +--m-metadata-column=$mmetadatacolumn + + +#if str($pmethod) != 'None': +--p-method=$pmethod +#end if + +#if $ppairwise: + --p-pairwise +#end if + +--p-permutations=$ppermutations + +--o-visualization=ovisualization + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp odistancematrix.qza $odistancematrix + +; +qiime tools export omantelscattervisualization.qzv --output-path out +&& mkdir -p '$omantelscattervisualization.files_path' +&& cp -r out/* '$omantelscattervisualization.files_path' +&& mv '$omantelscattervisualization.files_path/index.html' '$omantelscattervisualization' + +; +qiime tools export ovisualization.qzv --output-path out +&& mkdir -p '$ovisualization.files_path' +&& cp -r out/* '$ovisualization.files_path' +&& mv '$ovisualization.files_path/index.html' '$ovisualization' + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" /> + <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> + <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" /> + </repeat> + <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical sample metadata column. [required]" name="mmetadatacolumn" optional="False" type="text" /> + <param label="--p-method: " name="pmethod" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="permanova">permanova</option> + <option value="anosim">anosim</option> + <option value="permdisp">permdisp</option> + </param> + <param label="--p-pairwise: --p-pairwise: / --p-no-pairwise Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column. [default: False]" name="ppairwise" selected="False" type="boolean" /> + <param label="--p-permutations: INTEGER The number of permutations to be run when computing p-values. [default: 999]" name="ppermutations" optional="True" type="integer" value="999" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" /> + + </outputs> + + <help><![CDATA[ +Beta diversity group significance +############################################################### + +Determine whether groups of samples are significantly different from one +another using a permutation-based statistical test. + +Parameters +---------- +distance_matrix : DistanceMatrix + Matrix of distances between pairs of samples. +metadata : MetadataColumn[Categorical] + Categorical sample metadata column. +method : Str % Choices('permanova', 'anosim', 'permdisp'), optional + The group significance test to be applied. +pairwise : Bool, optional + Perform pairwise tests between all pairs of groups in addition to the + test across all groups. This can be very slow if there are a lot of + groups in the metadata column. +permutations : Int, optional + The number of permutations to be run when computing p-values. + +Returns +------- +visualization : Visualization + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file