Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_sample-classifier_classify-samples-from-dist.xml @ 14:a0a8d77a991c draft
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| author | florianbegusch |
|---|---|
| date | Thu, 03 Sep 2020 09:51:29 +0000 |
| parents | f190567fe3f6 |
| children |
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--- a/qiime2/qiime_sample-classifier_classify-samples-from-dist.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_sample-classifier_classify-samples-from-dist.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,85 +1,127 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_classify-samples-from-dist" name="qiime sample-classifier classify-samples-from-dist" version="2019.7"> - <description> - Run k-nearest-neighbors on a labeled distance matrix.</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<tool id="qiime_sample-classifier_classify-samples-from-dist" name="qiime sample-classifier classify-samples-from-dist" + version="2020.8"> + <description>Run k-nearest-neighbors on a labeled distance matrix.</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ qiime sample-classifier classify-samples-from-dist --i-distance-matrix=$idistancematrix ---m-metadata-column="$mmetadatacolumn" +# 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($input_files_mmetadatafile) +# end if -#if str($pk): - --p-k=$pk +#if '__ob__' in str($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 = $mmetadatacolumn_temp #end if -#if str($ppalette) != 'None': - --p-palette=$ppalette -#end if +--m-metadata-column=$mmetadatacolumn -#if $metadatafile: - --m-metadata-file=$metadatafile +--p-k=$pk + +#if str($ppalette) != 'None': +--p-palette=$ppalette #end if +--o-predictions=opredictions ---o-predictions=opredictions --o-accuracy-results=oaccuracyresults + +#if str($examples) != 'None': +--examples=$examples +#end if + ; -cp opredictions.qza $opredictions; -qiime tools export --input-path oaccuracyresults.qzv --output-path out && mkdir -p '$oaccuracyresults.files_path' +cp opredictions.qza $opredictions + +; +qiime tools export oaccuracyresults.qzv --output-path out +&& mkdir -p '$oaccuracyresults.files_path' && cp -r out/* '$oaccuracyresults.files_path' && mv '$oaccuracyresults.files_path/index.html' '$oaccuracyresults' - ]]></command> - <inputs> - <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix a distance matrix [required]" name="idistancematrix" optional="False" type="data"/> - <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text"/> - <param label="--p-k: INTEGER Number of nearest neighbors [default: 1]" name="pk" optional="True" type="integer" value="1"/> - <param label="--p-palette: " name="ppalette" optional="True" type="select"> - <option selected="True" value="None">Selection is Optional</option> - <option value="YellowOrangeBrown">YellowOrangeBrown</option> - <option value="YellowOrangeRed">YellowOrangeRed</option> - <option value="OrangeRed">OrangeRed</option> - <option value="PurpleRed">PurpleRed</option> - <option value="RedPurple">RedPurple</option> - <option value="BluePurple">BluePurple</option> - <option value="GreenBlue">GreenBlue</option> - <option value="PurpleBlue">PurpleBlue</option> - <option value="YellowGreen">YellowGreen</option> - <option value="summer">summer</option> - <option value="copper">copper</option> - <option value="viridis">viridis</option> - <option value="plasma">plasma</option> - <option value="inferno">inferno</option> - <option value="magma">magma</option> - <option value="sirocco">sirocco</option> - <option value="drifting">drifting</option> - <option value="melancholy">melancholy</option> - <option value="enigma">enigma</option> - <option value="eros">eros</option> - <option value="spectre">spectre</option> - <option value="ambition">ambition</option> - <option value="mysteriousstains">mysteriousstains</option> - <option value="daydream">daydream</option> - <option value="solano">solano</option> - <option value="navarro">navarro</option> - <option value="dandelions">dandelions</option> - <option value="deepblue">deepblue</option> - <option value="verve">verve</option> - <option value="greyscale">greyscale</option> - </param> - <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" /> + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix a distance matrix [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 metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text" /> + <param label="--p-k: INTEGER Number of nearest neighbors [default: 1]" name="pk" optional="True" type="integer" value="1" /> + <param label="--p-palette: " name="ppalette" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="YellowOrangeBrown">YellowOrangeBrown</option> + <option value="YellowOrangeRed">YellowOrangeRed</option> + <option value="OrangeRed">OrangeRed</option> + <option value="PurpleRed">PurpleRed</option> + <option value="RedPurple">RedPurple</option> + <option value="BluePurple">BluePurple</option> + <option value="GreenBlue">GreenBlue</option> + <option value="PurpleBlue">PurpleBlue</option> + <option value="YellowGreen">YellowGreen</option> + <option value="summer">summer</option> + <option value="copper">copper</option> + <option value="viridis">viridis</option> + <option value="cividis">cividis</option> + <option value="plasma">plasma</option> + <option value="inferno">inferno</option> + <option value="magma">magma</option> + <option value="sirocco">sirocco</option> + <option value="drifting">drifting</option> + <option value="melancholy">melancholy</option> + <option value="enigma">enigma</option> + <option value="eros">eros</option> + <option value="spectre">spectre</option> + <option value="ambition">ambition</option> + <option value="mysteriousstains">mysteriousstains</option> + <option value="daydream">daydream</option> + <option value="solano">solano</option> + <option value="navarro">navarro</option> + <option value="dandelions">dandelions</option> + <option value="deepblue">deepblue</option> + <option value="verve">verve</option> + <option value="greyscale">greyscale</option> + </param> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> - </inputs> - <outputs> - <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions"/> - <data format="html" label="${tool.name} on ${on_string}: accuracyresults.qzv" name="oaccuracyresults"/> - </outputs> - <help><![CDATA[ + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions" /> + <data format="html" label="${tool.name} on ${on_string}: accuracyresults.html" name="oaccuracyresults" /> + + </outputs> + + <help><![CDATA[ Run k-nearest-neighbors on a labeled distance matrix. -##################################################### +############################################################### Run k-nearest-neighbors on a labeled distance matrix. Return cross- validated (leave one out) predictions and accuracy. k = 1 by default @@ -92,7 +134,7 @@ Categorical metadata column to use as prediction target. k : Int, optional Number of nearest neighbors -palette : Str % Choices('YellowOrangeBrown', 'YellowOrangeRed', 'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue', 'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy', 'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream', 'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale'), optional +palette : Str % Choices('YellowOrangeBrown', 'YellowOrangeRed', 'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue', 'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'cividis', 'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy', 'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream', 'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale'), optional The color palette to use for plotting. Returns @@ -101,9 +143,9 @@ leave one out predictions for each sample accuracy_results : Visualization Accuracy results visualization. - ]]></help> -<macros> + ]]></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