Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_longitudinal_pairwise-distances.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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--- a/qiime2/qiime_longitudinal_pairwise-distances.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_longitudinal_pairwise-distances.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,27 +1,99 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_pairwise-distances" name="qiime longitudinal pairwise-distances" version="2019.7"> - <description> - Paired pairwise distance testing and boxplots</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<tool id="qiime_longitudinal_pairwise-distances" name="qiime longitudinal pairwise-distances" + version="2020.8"> + <description>Paired pairwise distance testing and boxplots</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ qiime longitudinal pairwise-distances --i-distance-matrix=$idistancematrix ---p-group-column="$pgroupcolumn" ---p-state-column="$pstatecolumn" ---p-state-1="$pstate1" ---p-state-2="$pstate2" +# 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($input_files_mmetadatafile) +# end if + +#if '__ob__' in str($pgroupcolumn): + #set $pgroupcolumn_temp = $pgroupcolumn.replace('__ob__', '[') + #set $pgroupcolumn = $pgroupcolumn_temp +#end if +#if '__cb__' in str($pgroupcolumn): + #set $pgroupcolumn_temp = $pgroupcolumn.replace('__cb__', ']') + #set $pgroupcolumn = $pgroupcolumn_temp +#end if +#if 'X' in str($pgroupcolumn): + #set $pgroupcolumn_temp = $pgroupcolumn.replace('X', '\\') + #set $pgroupcolumn = $pgroupcolumn_temp +#end if +#if '__sq__' in str($pgroupcolumn): + #set $pgroupcolumn_temp = $pgroupcolumn.replace('__sq__', "'") + #set $pgroupcolumn = $pgroupcolumn_temp +#end if +#if '__db__' in str($pgroupcolumn): + #set $pgroupcolumn_temp = $pgroupcolumn.replace('__db__', '"') + #set $pgroupcolumn = $pgroupcolumn_temp +#end if + +--p-group-column=$pgroupcolumn +#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 + + +--p-state-1=$pstate1 + +--p-state-2=$pstate2 + +#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 = $pindividualidcolumn_temp #end if -#if str($pindividualidcolumn): - --p-individual-id-column="$pindividualidcolumn" +#if '__db__' in str($pindividualidcolumn): + #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"') + #set $pindividualidcolumn = $pindividualidcolumn_temp #end if +--p-individual-id-column=$pindividualidcolumn #if $pparametric: @@ -29,78 +101,86 @@ #end if #if str($ppalette) != 'None': - --p-palette=$ppalette +--p-palette=$ppalette #end if #if str($preplicatehandling) != 'None': - --p-replicate-handling=$preplicatehandling +--p-replicate-handling=$preplicatehandling #end if - -#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($input_files_mmetadatafile) -#end if - - --o-visualization=ovisualization + +#if str($examples) != 'None': +--examples=$examples +#end if + ; -qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' +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'; - ]]></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"/> - <param label="--p-group-column: TEXT Metadata column on which to separate groups for comparison [required]" name="pgroupcolumn" optional="False" type="text"/> - <param label="--p-state-column: TEXT Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text"/> - <param label="--p-state-1: TEXT Baseline state column value. [required]" name="pstate1" optional="False" type="text"/> - <param label="--p-state-2: TEXT State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text"/> - <param label="--p-individual-id-column: TEXT Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state-1 or state-2, that subject will be dropped and reported in standard output by default. Set replicate_handling='random' to instead randomly select one member. [required]" name="pindividualidcolumn" optional="False" type="text"/> - <param label="--p-parametric: --p-no-parametric Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests. [default: False]" name="pparametric" selected="False" type="boolean"/> - <param label="--p-palette: " name="ppalette" optional="True" type="select"> - <option selected="True" value="None">Selection is Optional</option> - <option value="Set1">Set1</option> - <option value="Set2">Set2</option> - <option value="Set3">Set3</option> - <option value="Pastel1">Pastel1</option> - <option value="Pastel2">Pastel2</option> - <option value="Paired">Paired</option> - <option value="Accent">Accent</option> - <option value="Dark2">Dark2</option> - <option value="tab10">tab10</option> - <option value="tab20">tab20</option> - <option value="tab20b">tab20b</option> - <option value="tab20c">tab20c</option> - <option value="viridis">viridis</option> - <option value="plasma">plasma</option> - <option value="inferno">inferno</option> - <option value="magma">magma</option> - <option value="terrain">terrain</option> - <option value="rainbow">rainbow</option> - </param> - <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select"> - <option selected="True" value="None">Selection is Optional</option> - <option value="error">error</option> - <option value="random">random</option> - <option value="drop">drop</option> - </param> +&& mv '$ovisualization.files_path/index.html' '$ovisualization' - <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> - <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> - </repeat> - </inputs> - <outputs> - <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> - </outputs> - <help><![CDATA[ + ]]></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="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-group-column: TEXT Metadata column on which to separate groups for comparison [required]" name="pgroupcolumn" optional="False" type="text" /> + <param label="--p-state-column: TEXT Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text" /> + <param label="--p-state-1: TEXT Baseline state column value. [required]" name="pstate1" optional="False" type="text" /> + <param label="--p-state-2: TEXT State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text" /> + <param label="--p-individual-id-column: TEXT Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state-1 or state-2, that subject will be dropped and reported in standard output by default. Set replicate_handling=\'random\' to instead randomly select one member. [required]" name="pindividualidcolumn" optional="False" type="text" /> + <param label="--p-parametric: --p-parametric: / --p-no-parametric Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests. [default: False]" name="pparametric" selected="False" type="boolean" /> + <param label="--p-palette: " name="ppalette" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="Set1">Set1</option> + <option value="Set2">Set2</option> + <option value="Set3">Set3</option> + <option value="Pastel1">Pastel1</option> + <option value="Pastel2">Pastel2</option> + <option value="Paired">Paired</option> + <option value="Accent">Accent</option> + <option value="Dark2">Dark2</option> + <option value="tab10">tab10</option> + <option value="tab20">tab20</option> + <option value="tab20b">tab20b</option> + <option value="tab20c">tab20c</option> + <option value="viridis">viridis</option> + <option value="plasma">plasma</option> + <option value="inferno">inferno</option> + <option value="magma">magma</option> + <option value="terrain">terrain</option> + <option value="rainbow">rainbow</option> + <option value="cividis">cividis</option> + </param> + <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="error">error</option> + <option value="random">random</option> + <option value="drop">drop</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[ Paired pairwise distance testing and boxplots -############################################# +############################################################### Performs pairwise distance testing between sample pairs from each subject. Sample pairs may represent a typical intervention study, e.g., samples @@ -135,7 +215,7 @@ parametric : Bool, optional Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal- Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests. -palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional +palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow', 'cividis'), optional Color palette to use for generating boxplots. replicate_handling : Str % Choices('error', 'random', 'drop'), optional Choose how replicate samples are handled. If replicates are detected, @@ -145,10 +225,10 @@ Returns ------- -visualization : Visualization - ]]></help> -<macros> +visualization : Visualization + ]]></help> + <macros> <import>qiime_citation.xml</import> -</macros> -<expand macro="qiime_citation"/> -</tool> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file