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mda_heatmap_gen.xml |
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| diff -r 4ca62497d0a5 -r 63e3befddc8d mda_heatmap_gen.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mda_heatmap_gen.xml Thu Jan 19 15:17:48 2017 -0500 |
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| @@ -0,0 +1,142 @@ +<?xml version="1.0" encoding="UTF-8" ?> +<tool id="mda_heatmap_gen_toolshed" name="NG-CHM Generator" version="2.0.1"> + <description>Create Clustered Heat Maps</description> +<command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh '$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} + #for $op in $operations + ${op.class_name} + ${op.repeatinput.file_name} + ${op.cat} + #end for + '$output' + </command> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + <inputs> + <param name="inputmatrix" type="data" label="Input Matrix" /> + <param name="hmname" size="20" type="text" value="HM_name" label="User Defined Heat Map Name"/> + <param name="hmdesc" size="100" optional="true" type="text" value="_" label="Optional Heat Map Description"/> + <param name="summarymethod" type="select" label="Data Summarization Method"> + <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"> + <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"> + <option value="euclidean">Euclidean</option> + <option value="binary">Binary</option> + <option value="manhattan">Manhattan</option> + <option value="maximum">Maximum</option> + <option value="canberra">Canberra</option> + <option value="minkowski">Minkowski</option> + <option value="correlation">Correlation</option> + </param> + <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: 'average' for Average Linkage, 'complete' for Complete Linkage, 'single' for Single Linkage, 'ward', 'mcquitty', 'median', or 'centroid'."> + <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> + <option value="centroid">Centroid</option> + </param> + <param name="rowDendroCut" type="select" label="Create row categorical covariate bar based on number of top-level dendrogram clusters" > + <option value="0" selected="true" >None</option> + <option value="2" >2</option> + <option value="3" >3</option> + <option value="4" >4</option> + <option value="5" >5</option> + <option value="6" >6</option> + <option value="7" >7</option> + <option value="8" >8</option> + <option value="9" >9</option> + <option value="10" >10</option> + </param> + </when> + </conditional> + <conditional name="d_cols"> + <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random"> + <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"> + <option value="euclidean">Euclidean</option> + <option value="binary">Binary</option> + <option value="manhattan">Manhattan</option> + <option value="maximum">Maximum</option> + <option value="canberra">Canberra</option> + <option value="minkowski">Minkowski</option> + <option value="correlation">Correlation</option> + </param> + <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="Choices: 'average' for Average Linkage, 'complete' for Complete Linkage, 'single' for Single Linkage, 'ward', 'mcquitty', 'median', or 'centroid'."> + <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> + <option value="centroid">Centroid</option> + </param> + <param name="colDendroCut" type="select" label="Create column categorical covariate bar based on number of top-level dendrogram clusters" > + <option value="0" selected="true" >None</option> + <option value="2" >2</option> + <option value="3" >3</option> + <option value="4" >4</option> + <option value="5" >5</option> + <option value="6" >6</option> + <option value="7" >7</option> + <option value="8" >8</option> + <option value="9" >9</option> + <option value="10" >10</option> + </param> + </when> + </conditional> + <repeat name="operations" title="Covariate Bars"> + <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name"> + <sanitizer invalid_char="_"> + <valid initial="none"> + <add preset="string.letters"/> + <add preset="string.digits"/> + </valid> + <mapping initial="none"> + </mapping> + </sanitizer> + </param> + <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/> + <param name="cat" type="select" label="Axis Covariate Type"> + <option value="row_categorical" >row categorical</option> + <option value="row_continuous" >row continuous</option> + <option value="column_categorical" >column categorical</option> + <option value="column_continuous" >column continuous</option> + </param> + </repeat> + </inputs> + <outputs> + <data name="output" label='${hmname}' format="ngchm"/> + </outputs> + <tests> + <test> + <param name="inputmatrix" value="400x400.txt" /> + <param name="hmname" value="testRun" /> + <param name="$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> |