Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced
view mda_advanced_heatmap_gen.xml @ 0:8893ea2915cc draft
Initial Version of Advanced Heat Map Tool
author | insilico-bob |
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date | Tue, 08 Aug 2017 14:01:05 -0400 |
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children | 603f99d9e776 |
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<?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>