Mercurial > repos > md-anderson-bioinformatics > heat_map_creation
diff mda_heatmap_gen.xml @ 38:605ec840a06b draft
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| author | insilico-bob |
|---|---|
| date | Thu, 20 Jun 2019 11:30:12 -0400 |
| parents | f2272e907f1b |
| children |
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--- a/mda_heatmap_gen.xml Thu Nov 08 14:59:04 2018 -0500 +++ b/mda_heatmap_gen.xml Thu Jun 20 11:30:12 2019 -0400 @@ -2,16 +2,17 @@ <tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.3"> <requirements> <requirement type="package" version="3.4.1">r-base</requirement> - <requirement type="package" version="8">openjdk</requirement> + <requirement type="package" version="8.0.144">openjdk</requirement> </requirements> <description>Create Clustered Heat Maps</description> - <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh "standard" "Heat_Map_$hmname" "$hmdesc" '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__;$__tool_data_path__/' 0 0 labels labels 'None' + <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh "$__tool_directory__" "$__tool_data_path__/" "chm_name|Heat_Map_$hmname" "chm_description|$hmdesc" + "matrix_files|path|$inputmatrix|name|datalayer|summary_method|$summarymethod" + "row_configuration|order_method|${d_rows.rowOrderMethod}|distance_metric|${d_rows.rowDistanceMeasure}|agglomeration_method|${d_rows.rowAgglomerationMethod}|tree_covar_cuts|0|data_type|labels" + "col_configuration|order_method|${d_cols.columnOrderMethod}|distance_metric|${d_cols.columnDistanceMeasure}|agglomeration_method|${d_cols.columnAgglomerationMethod}|tree_covar_cuts|0|data_type|labels" #for $op in $operations - '${op.class_name}' - '${op.repeatinput.file_name}' - '${op.cat}' - #end for - '$output' + 'classification|name|${op.class_name}|path|${op.repeatinput.file_name}|category|${op.cat}' + #end for + 'output_location|$output' </command> <stdio> <exit_code range="1:" level="fatal" /> @@ -22,11 +23,6 @@ <sanitizer> <valid> <add preset="string.printable"/> -<!-- <add value="string.letters"/> - <add value="string.digits"/> - <add value="-"/> - <add value="_"/> ---> <remove value="""/> <remove value="'"/> <remove value=" "/> @@ -59,12 +55,12 @@ <when value="Hierarchical"> <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="For clustering, select the method of determining distance between rows"> <option value="euclidean">Euclidean</option> - <option value="binary">Binary</option> + <!-- <option value="binary">Binary</option> ** breaks dendrogram --> <option value="manhattan">Manhattan</option> <option value="maximum">Maximum</option> - <option value="canberra">Canberra</option> + <!-- <option value="canberra">Canberra</option> ** breaks dendrogram --> <option value="minkowski">Minkowski</option> - <option value="correlation">Correlation</option> + <!-- <option value="correlation">Correlation</option> ** breaks dendrogram --> </param> <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="For clustering, select algorithm for building clusters."> <option value="average">Average Linkage</option> @@ -72,8 +68,8 @@ <option value="single">Single Linkage</option> <option value="ward" selected="true">Ward</option> <option value="mcquitty">Mcquitty</option> - <option value="median">Median</option> - <option value="centroid">Centroid</option> + <!-- <option value="median">Median</option> ** breaks dendrogram + <option value="centroid">Centroid</option> ** breaks dendrogram --> </param> </when> <when value="Original"> @@ -94,12 +90,12 @@ <when value="Hierarchical"> <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="For clustering, select the method of determining distance between columns"> <option value="euclidean">Euclidean</option> - <option value="binary">Binary</option> + <!-- <option value="binary">Binary</option> ** breaks dendrogram --> <option value="manhattan">Manhattan</option> <option value="maximum">Maximum</option> - <option value="canberra">Canberra</option> + <!-- <option value="canberra">Canberra</option> ** breaks dendrogram --> <option value="minkowski">Minkowski</option> - <option value="correlation">Correlation</option> + <!-- <option value="correlation">Correlation</option> ** breaks dendrogram --> </param> <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="For clustering, select algorithm for building clusters."> <option value="average">Average Linkage</option> @@ -107,8 +103,8 @@ <option value="single">Single Linkage</option> <option value="ward" selected="true">Ward</option> <option value="mcquitty">Mcquitty</option> - <option value="median">Median</option> - <option value="centroid">Centroid</option> + <!-- <option value="median">Median</option> ** breaks dendrogram + <option value="centroid">Centroid</option> ** breaks dendrogram --> </param> </when> <when value="Original"> @@ -133,9 +129,9 @@ </param> <param name="repeatinput" type="data" format="Tabular" label="Covariate File" help="Tab delimited text file with row or column label and covariate value on each line."/> <param name="cat" type="select" label="Axis Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values."> - <option value="row_categorical" >Row Categorical</option> + <option value="row_discrete" >Row Categorical</option> <option value="row_continuous" >Row Continuous</option> - <option value="column_categorical" >Column Categorical</option> + <option value="column_discrete" >Column Categorical</option> <option value="column_continuous" >Column Continuous</option> </param> </repeat>