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view mda_advanced_heatmap_gen.xml @ 4:d747292c486f draft
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| author | insilico-bob |
|---|---|
| date | Tue, 06 Nov 2018 16:30:12 -0500 |
| parents | 9359e0a0d40b |
| children | 15c71ed09efa |
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<?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> <requirement type="package" version="8.0.144">openjdk</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 " #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="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="""/> <remove value="'"/> <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="""/> <remove value="'"/> <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> <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="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label."> <sanitizer> <valid> <add preset="string.printable"/> <remove value="""/> <remove value="'"/> <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> <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>