Mercurial > repos > md-anderson-bioinformatics > heat_map_creation
diff mda_heatmap_gen.xml @ 33:0097750ad7ad draft
Version 2.2.1 embedded viewer
author | insilico-bob |
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date | Tue, 05 Dec 2017 14:57:34 -0500 |
parents | 16593e40c2cd |
children | 58437af2d675 |
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--- a/mda_heatmap_gen.xml Thu Jul 20 15:31:06 2017 -0400 +++ b/mda_heatmap_gen.xml Tue Dec 05 14:57:34 2017 -0500 @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8" ?> -<tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.0.5"> +<tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.1.1"> <description>Create Clustered Heat Maps</description> <!-- <command interpreter="python" detect_errors="aggressive">$__tool_directory__/mda_heatmap_gen.py 'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' 0 0 labels labels 'None'--> - <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh "Heat_Map_$hmname" "$hmdesc" '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__/' 0 0 labels labels 'None' + <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__/' 0 0 labels labels 'None' #for $op in $operations ${op.class_name} ${op.repeatinput.file_name} @@ -14,22 +14,22 @@ <exit_code range="1:" level="fatal" /> </stdio> <inputs> - <param name="inputmatrix" type="data" format="Tabular" label="Input Matrix" /> - <param name="hmname" size="20" type="text" value="Heat_Map_name" label="User Defined Heat Map Name"/> - <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="User Defined Heat Map Description"/> - <param name="summarymethod" type="select" label="Data Summarization Method"> + <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data." /> + <param name="hmname" size="20" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/> + <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="Heat Map Description" help="Longer description of the heat map contents."/> + <param name="summarymethod" type="select" label="Data Summarization Method" help="For large matrices, the selected method is used to aggregate data values in the summary view."> <option value="average">Average</option> <option value="sample">Sample</option> <option value="mode">Mode</option> </param> - <conditional name="d_rows"> - <param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random"> + <conditional name="d_rows"> + <param name="rowOrderMethod" type="select" label="Row ordering method" help="Determine if rows should be clustered, randomized, or remain as is."> <option value="Hierarchical">Hierarchical Clustering</option> <option value="Original">Original Order</option> <option value="Random">Random</option> </param> <when value="Hierarchical"> - <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation"> + <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="manhattan">Manhattan</option> @@ -38,7 +38,7 @@ <option value="minkowski">Minkowski</option> <option value="correlation">Correlation</option> </param> - <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'."> + <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="For clustering, select algorithm for building clusters."> <option value="average">Average Linkage</option> <option value="complete">Complete Linkage</option> <option value="single">Single Linkage</option> @@ -58,13 +58,13 @@ </when> </conditional> <conditional name="d_cols"> - <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random"> + <param name="columnOrderMethod" type="select" label="Column ordering method" help="Determine if columns should be clustered, randomized, or remain as is."> <option value="Hierarchical">Hierarchical Clustering</option> <option value="Original">Original Order</option> <option value="Random">Random</option> </param> <when value="Hierarchical"> - <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation"> + <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="manhattan">Manhattan</option> @@ -73,7 +73,7 @@ <option value="minkowski">Minkowski</option> <option value="correlation">Correlation</option> </param> - <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'."> + <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="For clustering, select algorithm for building clusters."> <option value="average">Average Linkage</option> <option value="complete">Complete Linkage</option> <option value="single">Single Linkage</option> @@ -93,7 +93,7 @@ </when> </conditional> <repeat name="operations" title="Covariate Bars"> - <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name"> + <param name="class_name" size="20" type="text" value="" label="Covariate Name" help="Label for the covariate to display in the heat map."> <sanitizer invalid_char="_"> <valid initial="none"> <add preset="string.letters"/> @@ -103,8 +103,8 @@ </mapping> </sanitizer> </param> - <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/> - <param name="cat" type="select" label="Axis Covariate Type"> + <param name="repeatinput" type="data" format="text" 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_continuous" >Row Continuous</option> <option value="column_categorical" >Column Categorical</option>