| Previous changeset 63:17085324d26f (2017-01-09) Next changeset 65:d6e1d60acdcb (2017-01-09) |
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Commit message:
Deleted selected files |
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removed:
NGCHMheatmap.xml |
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| diff -r 17085324d26f -r 47e427504fde NGCHMheatmap.xml --- a/NGCHMheatmap.xml Mon Jan 09 10:13:19 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,87 +0,0 @@ -<?xml version="1.0" encoding="UTF-8" ?> -<tool id="NGCHMheatmap" name="NGCHM Heatmap" version="4.2.1"> - <description>Create Dynamic Clustered HeatMap from Matrix and Covariate files</description> - <requirements> - <requirement type="package" >ngchm_dependencies</requirement> - </requirements> - <command detect_errors="aggressive">$GALAXY_ROOT_DIR/config/plugins/visualizations/MDAheatmap/ngchm-software/heatmap.sh '$hmname' '$hmdesc' '$inputmatrix' $rowOrderMethod $rowDistanceMeasure $rowAgglomerationMethod $columnOrderMethod $columnDistanceMeasure $columnAgglomerationMethod '$summarymethod' '$GALAXY_ROOT_DIR/tools/MDA_Heatmaps/' - #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 HeatMap Name"/> - <param name="hmdesc" size="100" optional="true" type="text" value="_" label="Optional HeatMap 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> - <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> - <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">Ward</option> - <option value="mcquitty">Mcquitty</option> - <option value="median">Median</option> - <option value="centroid">Centroid</option> - </param> - <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> - <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">Ward</option> - <option value="mcquitty">Mcquitty</option> - <option value="median">Median</option> - <option value="centroid">Centroid</option> - </param> - <repeat name="operations" title="Covariate Bars"> - <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name"/> - <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="zip"/> - </outputs> -</tool> |