comparison mda_heatmap_gen.xml @ 33:0097750ad7ad draft

Version 2.2.1 embedded viewer

32:16593e40c2cd

<?xml version="1.0" encoding="UTF-8" ?>
<tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.0.5">
  <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'
    #for $op in $operations
       ${op.class_name}
       ${op.repeatinput.file_name}
       ${op.cat}
      #end for

 </command>
	<stdio>
      <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">
		<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 Linkage, Complete Linkage,  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>	    

		    <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="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 Linkage, Complete Linkage,  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>	    

		    <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="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>

33:0097750ad7ad

<?xml version="1.0" encoding="UTF-8" ?>
<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">$__tool_directory__/heatmap.sh  "standard" "Heat_Map_$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}
       ${op.cat}
      #end for

 </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="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="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>
				<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="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>	    

		    <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>
				<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="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>	    

		    <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="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"/>
                <add preset="string.digits"/>
              </valid>
              <mapping initial="none">
              </mapping>
           </sanitizer>
        </param>
        <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>
	  <option value="column_continuous" >Column Continuous</option>
	</param>