Mercurial > repos > md-anderson-bioinformatics > heat_map_creation
diff mda_heatmap_gen.xml @ 40:8f8ab332a050 draft
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| author | insilico-bob |
|---|---|
| date | Thu, 20 Jun 2019 11:39:46 -0400 |
| parents | |
| children | 8acca16f3921 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mda_heatmap_gen.xml Thu Jun 20 11:39:46 2019 -0400 @@ -0,0 +1,159 @@ +<?xml version="1.0" encoding="UTF-8" ?> +<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="8.0.144">openjdk</requirement> + </requirements> + <description>Create Clustered Heat Maps</description> + <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 $operations + 'classification|name|${op.class_name}|path|${op.repeatinput.file_name}|category|${op.cat}' + #end for + 'output_location|$output' + </command> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + <inputs> + <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="40" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/> + <sanitizer> + <valid> + <add preset="string.printable"/> + <remove value="""/> + <remove value="'"/> + <remove value=" "/> + </valid> + </sanitizer> + <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."/> + <sanitizer> + <valid> + <add preset="string.printable"/> + <add value="string.letters"/> + <add value="string.digits"/> + <add value="-"/> + <add value="_"/> + <remove value="""/> + <remove value="'"/> + <remove value=" "/> + </valid> + </sanitizer> + <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="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="For clustering, select the method of determining distance between rows"> + <option value="euclidean">Euclidean</option> + <!-- <option value="binary">Binary</option> ** breaks dendrogram --> + <option value="manhattan">Manhattan</option> + <option value="maximum">Maximum</option> + <!-- <option value="canberra">Canberra</option> ** breaks dendrogram --> + <option value="minkowski">Minkowski</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> + <option value="complete">Complete Linkage</option> + <option value="single">Single Linkage</option> + <option value="ward" selected="true">Ward</option> + <option value="mcquitty">Mcquitty</option> + <!-- <option value="median">Median</option> ** breaks dendrogram + <option value="centroid">Centroid</option> ** breaks dendrogram --> + </param> + </when> + <when value="Original"> + <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> + <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> + </when> + <when value="Random"> + <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> + <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> + </when> + </conditional> + <conditional name="d_cols"> + <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="For clustering, select the method of determining distance between columns"> + <option value="euclidean">Euclidean</option> + <!-- <option value="binary">Binary</option> ** breaks dendrogram --> + <option value="manhattan">Manhattan</option> + <option value="maximum">Maximum</option> + <!-- <option value="canberra">Canberra</option> ** breaks dendrogram --> + <option value="minkowski">Minkowski</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> + <option value="complete">Complete Linkage</option> + <option value="single">Single Linkage</option> + <option value="ward" selected="true">Ward</option> + <option value="mcquitty">Mcquitty</option> + <!-- <option value="median">Median</option> ** breaks dendrogram + <option value="centroid">Centroid</option> ** breaks dendrogram --> + </param> + </when> + <when value="Original"> + <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> + <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> + </when> + <when value="Random"> + <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> + <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> + </when> + </conditional> + <repeat name="operations" title="Covariate Bars"> + <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label."> + <sanitizer> + <valid> + <add preset="string.printable"/> + <remove value="""/> + <remove value="'"/> + <remove value=" "/> + </valid> + </sanitizer> + </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_discrete" >Row Categorical</option> + <option value="row_continuous" >Row Continuous</option> + <option value="column_discrete" >Column Categorical</option> + <option value="column_continuous" >Column Continuous</option> + </param> + </repeat> + </inputs> + <outputs> + <data name="output" label='Heat_Map_$hmname' format="ngchm"/> + </outputs> + <tests> + <test> + <param name="inputmatrix" value="400x400.txt" /> + <param name="hmname" value="testRun" /> + <param name="$hmdesc" value="validateTool" /> + <param name="summarymethod" value="Average" /> + <param name="rowOrderMethod" value="Hierarchical" /> + <param name="rowDistanceMeasure" value="Manhattan" /> + <param name="rowAgglomerationMethod" value="Ward" /> + <param name="columnOrderMethod" value="Hierarchical" /> + <param name="columnDistanceMeasure" value="Manhattan" /> + <param name="columnAgglomerationMethod" value="Ward" /> + <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" /> + + </test> +<!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied --> + </tests> + </tool>