comparison mda_heatmap_gen.xml @ 32:16593e40c2cd draft

Version 2.0.5

31:e01b833f5d43

<?xml version="1.0" encoding="UTF-8" ?>
<tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.0.2">
  <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} $rowDataType $colDataType
    #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="text" 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' 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>
        <when value="Original">
		    <param name="rowDistanceMeasure" type="text" size="0"     value="n/a"/>
		    <param name="rowAgglomerationMethod" type="text" size="0"     value="n/a"/>
		    <param name="rowDendroCut" size="0"   type="text" value="0"/>
        </when>
        <when value="Random">
		    <param name="rowDistanceMeasure" type="text" size="0"     value="n/a"/>
		    <param name="rowAgglomerationMethod" type="text" size="0"     value="n/a"/>
		    <param name="rowDendroCut" type="text" size="0"    value="0"/>
        </when>
    </conditional>
    <param name="rowDataType" type="select" label="Linkouts to row data type info" >
        <option value="labels" selected="true" >None</option>
        <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
        <option value="bio.feature.agilent" >Agilent Id</option>
        <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
        <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
        <option value="bio.gene.entrez" >Gene Entrez Id</option>
        <option value="bio.gene.hugo" >Gene HUGO symbol</option>
        <option value="bio.go" >Gene Ontology (GO) Id</option>
        <option value="bio.geo.acc" >GEO Accession Id</option>
        <option value="bio.probe.illumina" >Illumina Probe Id</option>
        <option value="bio.probe.infinium" >Infinium Probe Id</option>
        <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
        <option value="bio.mirna" >miRNA Id</option>
        <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
        <option value="bio.pubmed" >Pubmed Id</option>
        <option value="bio.pubmed.search" >Pubmed Search Term</option>
        <option value="scholar" >Scholarly term</option>
        <option value="bio.gene.unigene" >Unigene CID</option>
        <option value="bio.protein.uniprot" >UniProt Id</option>
    </param>    
	<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>
        <when value="Original">
		    <param name="columnDistanceMeasure" type="text" size="0"     value="n/a"/>
		    <param name="columnAgglomerationMethod" type="text" size="0"     value="n/a"/>
		    <param name="colDendroCut" type="text" size="0"     value="0"/>
        </when>
        <when value="Random">
		    <param name="columnDistanceMeasure" type="text" size="0"     value="n/a"/>
		    <param name="columnAgglomerationMethod" type="text" size="0"     value="n/a"/>
		    <param name="colDendroCut" type="text" size="0"     value="0"/>
        </when>
    </conditional>
    <param name="colDataType" type="select" label="Linkouts to column data type info" >
        <option value="labels" selected="true" >None</option>
        <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
        <option value="bio.feature.agilent" >Agilent Id</option>
        <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
        <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
        <option value="bio.gene.entrez" >Gene Entrez Id</option>
        <option value="bio.gene.hugo" >Gene HUGO symbol</option>
        <option value="bio.go" >Gene Ontology (GO) Id</option>
        <option value="bio.geo.acc" >GEO Accession Id</option>
        <option value="bio.probe.illumina" >Illumina Probe Id</option>
        <option value="bio.probe.infinium" >Infinium Probe Id</option>
        <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
        <option value="bio.mirna" >miRNA Id</option>
        <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
        <option value="bio.pubmed" >Pubmed Id</option>
        <option value="bio.pubmed.search" >Pubmed Search Term</option>
        <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="Axis Covariate Name">
           <sanitizer invalid_char="_">
              <valid initial="none">
                <add preset="string.letters"/>

              </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>

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>	    
				<option value="median">Median</option>	    
				<option value="centroid">Centroid</option>	    
			</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="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>	    
				<option value="median">Median</option>	    
				<option value="centroid">Centroid</option>	    
			</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="20" type="text" value="" label="Axis Covariate Name">
           <sanitizer invalid_char="_">
              <valid initial="none">
                <add preset="string.letters"/>

              </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='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>