comparison mda_advanced_heatmap_gen.xml @ 2:19382473a76b draft

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1:603f99d9e776

<?xml version="1.0" encoding="UTF-8" ?>
<tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.1.1">
  <description> Create Clustered Heat Maps</description>
<!-- command interpreter="python" detect_errors="aggressive">$__tool_directory__/mad_advanced_heatmap_gen.py  'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType  -->
<command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.sh  'advanced' '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__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType 'c_${d_rows.rcutrows.rowDendroTreeCut}' 'c_${d_cols.ccutrows.colDendroTreeCut}' 't_$rowTopItems' 't_$colTopItems' 

    "
    #for $attr in $hm_attribute
      ${attr.attrbute_key}:${attr.attrbute_value};
    #end for

	<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>

        <option value="scholar" >Scholarly term</option>
        <option value="bio.gene.unigene" >Unigene CId</option>
        <option value="bio.protein.uniprot" >UniProt Id</option>
    </param>    
    <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."/>
        <conditional name="cattype">
			<param name="cat" type="select" label="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>

2:19382473a76b

<?xml version="1.0" encoding="UTF-8" ?>
<tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.3">
  <requirements>
    <requirement type="package" version="3.4.1">r-base</requirement> 
  </requirements>
  <description> Create Clustered Heat Maps with Advanced Options</description>
<command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.sh  'advanced' 'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__;$__tool_data_path__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType 'c_${d_rows.rcutrows.rowDendroTreeCut}' 'c_${d_cols.ccutrows.colDendroTreeCut}' 't_$rowTopItems' 't_$colTopItems' 

    "
    #for $attr in $hm_attribute
      ${attr.attrbute_key}:${attr.attrbute_value};
    #end for

	<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="&quot;"/>
            	<remove value="&apos;"/>
                <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"/>
            	<remove value="&quot;"/>
            	<remove value="&apos;"/>
                <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>

        <option value="scholar" >Scholarly term</option>
        <option value="bio.gene.unigene" >Unigene CId</option>
        <option value="bio.protein.uniprot" >UniProt Id</option>
    </param>    
    <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="&quot;"/>
            	<remove value="&apos;"/>
                <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."/>
        <conditional name="cattype">
			<param name="cat" type="select" label="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>