Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced
diff mda_advanced_heatmap_gen.xml @ 1:603f99d9e776 draft
Version 2.2.1 embedded viewer
| author | insilico-bob |
|---|---|
| date | Tue, 05 Dec 2017 14:59:26 -0500 |
| parents | 8893ea2915cc |
| children | 19382473a76b |
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--- a/mda_advanced_heatmap_gen.xml Tue Aug 08 14:01:05 2017 -0400 +++ b/mda_advanced_heatmap_gen.xml Tue Dec 05 14:59:26 2017 -0500 @@ -1,220 +1,361 @@ -<?xml version="1.0" encoding="UTF-8" ?> -<tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.0.5"> - <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 '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 - - " - #for $attr in $hm_attribute - ${attr.attrbute_key}:${attr.attrbute_value}; - #end for - " - - #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" 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> - <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" hidden="true" value="n/a"/> - <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> - <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/> - </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"/> - <param name="rowDendroCut" type="text" size="0" hidden="true" 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.cbioportal.sampleid" >cBioPortal sample 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.pathway.mdanderson" >MD Anderson pathway Id</option> - <option value="bio.mirna" >miRNA Id</option> - <option value="bio.pubmed.search" >Pubmed Search Term</option> - <option value="scholar" >Scholarly term</option> - <option value="bio.protein.uniprotid" >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 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> - <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" hidden="true" value="n/a"/> - <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> - <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/> - </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"/> - <param name="colDendroCut" type="text" size="0" hidden="true" 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.cbioportal.sampleid" >cBioPortal sample 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.pathway.mdanderson" >MD Anderson pathway Id</option> - <option value="bio.mirna" >miRNA Id</option> - <option value="bio.pubmed.search" >Pubmed Search Term</option> - <option value="scholar" >Scholarly term</option> - <option value="bio.protein.uniprotid" >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"/> - <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> - <repeat name="hm_attribute" title="Heat Map Attributes"> - <param name="attrbute_key" size="50" type="text" value="" label="Heat Map Attributes json pair-- key "> - <sanitizer invalid_char="_"> - <valid initial=""> - <add preset="string.letters"/> - <add preset="string.digits"/> - </valid> - <mapping initial=""> - </mapping> - </sanitizer> - </param> - <param name="attrbute_value" size="50" type="text" label="Heat Map Attributes json pairs -- value "> - <sanitizer invalid_char="_"> - <valid initial=""> - <add preset="string.letters"/> - <add preset="string.digits"/> - </valid> - <mapping initial=""> - </mapping> - </sanitizer> - </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> - </tool> +<?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 + " + + #for $op in $operations + ${op.class_name} + ${op.repeatinput.file_name} + ${op.cattype.cat} + ${op.cattype.bartype} + #end for + '$output' + </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> + <option value="median">Median</option> + <option value="centroid">Centroid</option> + </param> + <param name="rowDendroCut" type="select" label="Row Cluster Covariate Bar" help="To generate a row covariate bar based on clusters, select the number of clusters(classes) to use."> + <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> + <conditional name="rcutrows"> + <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> + <option value="none">None</option> + <option value="treecuts">Cluster-Based Gaps</option> + <option value="positional">Fixed Gaps</option> + </param> + <when value="none"> + <param name="rowDendroTreeCut" type="text" size="0" hidden="true" value="0"/> + </when> + <when value="treecuts"> + <param name="rowDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters." > + <option value="0t" selected="true" >None</option> + <option value="2t" >2</option> + <option value="3t" >3</option> + <option value="4t" >4</option> + <option value="5t" >5</option> + <option value="6t" >6</option> + <option value="7t" >7</option> + <option value="8t" >8</option> + <option value="9t" >9</option> + <option value="10t" >10</option> + </param> + </when> + <when value="positional"> + <param name="rowDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/> + </when> + </conditional> + </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"/> + <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/> + <conditional name="rcutrows"> + <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> + <option value="none">None</option> + <option value="positional">Fixed Gaps</option> + </param> + <when value="none"> + <param name="rowDendroTreeCut" type="text" size="100" value="None" hidden="true"/> + </when> + <when value="positional"> + <param name="rowDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/> + </when> + </conditional> + </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"/> + <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/> + <conditional name="rcutrows"> + <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> + <option value="none">None</option> + <option value="positional">Fixed Gaps</option> + </param> + <when value="none"> + <param name="rowDendroTreeCut" type="text" size="100" value="None" hidden="true"/> + </when> + <when value="positional"> + <param name="rowDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/> + </when> + </conditional> + </when> + </conditional> + <param name="rowTopItems" size="100" type="text" value="None" label="Row Top Items" help="A few rows can be labeled in the full summary heat map. To do so provide a comma delimited list of row labels."/> + <param name="rowDataType" type="select" label="Row Label Type" help="Enable label driven link-outs by specifying the type of row labels."> + <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="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> + <option value="median">Median</option> + <option value="centroid">Centroid</option> + </param> + <param name="colDendroCut" type="select" label="Column Cluster Covariate Bar" help="To generate a column covariate bar based on clusters, select the number of clusters(classes) to use."> + <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> + <conditional name="ccutrows"> + <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> + <option value="none">None</option> + <option value="treecuts">Cluster-Based Gaps</option> + <option value="positional">Fixed Gaps</option> + </param> + <when value="none"> + <param name="colDendroTreeCut" type="text" size="0" hidden="true" value="0"/> + </when> + <when value="treecuts"> + <param name="colDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters."> + <option value="0t" selected="true" >None</option> + <option value="2t" >2</option> + <option value="3t" >3</option> + <option value="4t" >4</option> + <option value="5t" >5</option> + <option value="6t" >6</option> + <option value="7t" >7</option> + <option value="8t" >8</option> + <option value="9t" >9</option> + <option value="10t" >10</option> + </param> + </when> + <when value="positional"> + <param name="colDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/> + </when> + </conditional> + </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"/> + <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/> + <conditional name="ccutrows"> + <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> + <option value="none">None</option> + <option value="positional">Fixed Gaps</option> + </param> + <when value="none"> + <param name="colDendroTreeCut" type="text" size="100" value="None" hidden="true"/> + </when> + <when value="positional"> + <param name="colDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/> + </when> + </conditional> + </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"/> + <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/> + <conditional name="ccutrows"> + <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> + <option value="none">None</option> + <option value="positional">Fixed Gaps</option> + </param> + <when value="none"> + <param name="colDendroTreeCut" type="text" size="100" value="None" hidden="true"/> + </when> + <when value="positional"> + <param name="colDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/> + </when> + </conditional> + </when> + </conditional> + <param name="colTopItems" size="100" type="text" value="None" label="Column Top Items" help="A few columns can be labeled in the full summary heat map. To do so provide a comma delimited list of column labels."/> + <param name="colDataType" type="select" label="Column Label Type" help="Enable label driven link-outs by specifying the type of column labels."> + <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="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> + <option value="column_continuous" >Column Continuous</option> + </param> + <when value="row_continuous"> + <param name="bartype" type="select" label="Display Type"> + <option value="color_plot" >Standard</option> + <option value="bar_plot" >Bar Plot</option> + <option value="scatter_plot" >Scatter Plot</option> + </param> + </when> + <when value="column_continuous"> + <param name="bartype" type="select" label="Display Type"> + <option value="color_plot" >Standard</option> + <option value="bar_plot" >Bar Plot</option> + <option value="scatter_plot" >Scatter Plot</option> + </param> + </when> + <when value="column_categorical"> + <param name="bartype" type="text" hidden="true" value="color_plot"/> + </when> + <when value="row_categorical"> + <param name="bartype" type="text" hidden="true" value="color_plot"/> + </when> + </conditional> + </repeat> + <repeat name="hm_attribute" title="Heat Map Attributes"> + <param name="attrbute_key" size="50" type="text" value="" label="Heat Map Attribute Key" help="For map level attributes. Enter the key (no spaces)."> + <sanitizer invalid_char="_"> + <valid initial=""> + <add preset="string.letters"/> + <add preset="string.digits"/> + </valid> + <mapping initial=""> + </mapping> + </sanitizer> + </param> + <param name="attrbute_value" size="50" type="text" label="Heat Map Attributes Value" help="For map level attributes. Enter the value (no spaces)."> + <sanitizer invalid_char="_"> + <valid initial=""> + <add preset="string.letters"/> + <add preset="string.digits"/> + </valid> + <mapping initial=""> + </mapping> + </sanitizer> + </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> + </tool>