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mda_heatmap_gen.xml |
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| diff -r 82dc9267b8b5 -r 46061edf0db4 mda_heatmap_gen.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mda_heatmap_gen.xml Fri Jan 27 11:32:40 2017 -0500 |
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| b'@@ -0,0 +1,204 @@\n+<?xml version="1.0" encoding="UTF-8" ?>\n+<tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.0.2">\n+ <description>Create Clustered Heat Maps</description>\n+<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\n+ #for $op in $operations\n+ ${op.class_name}\n+ ${op.repeatinput.file_name}\n+ ${op.cat}\n+ #end for\n+ \t\'$output\' \n+ </command>\n+\t<stdio>\n+ <exit_code range="1:" level="fatal" />\n+\t</stdio>\n+ <inputs>\n+ <param name="inputmatrix" type="data" label="Input Matrix" />\n+ <param name="hmname" size="20" type="text" value="Heat_Map_name" label="User Defined Heat Map Name"/>\n+ <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="User Defined Heat Map Description"/>\n+ <param name="summarymethod" \ttype="select" label="Data Summarization Method">\n+\t\t<option value="average">average</option>\n+\t\t<option value="sample">sample</option>\n+\t\t<option value="mode">mode</option>\n+ </param>\n+ <conditional name="d_rows">\n+\t<param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">\n+\t\t<option value="Hierarchical">Hierarchical Clustering</option>\n+\t\t<option value="Original">Original Order</option>\t \n+\t\t<option value="Random">Random</option>\t \n+\t</param>\n+ <when value="Hierarchical">\n+\t<param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="euclidean, binary, manhattan, maximum, canberra, minkowski, or correlation">\n+\t\t<option value="euclidean">Euclidean</option>\n+\t\t<option value="binary">Binary</option>\n+\t\t<option value="manhattan">Manhattan</option>\n+\t\t<option value="maximum">Maximum</option>\n+\t\t<option value="canberra">Canberra</option>\t \n+\t\t<option value="minkowski">Minkowski</option>\t \n+\t\t<option value="correlation">Correlation</option>\t \n+\t</param>\n+\t<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\'.">\n+\t\t<option value="average">Average Linkage</option>\n+\t\t<option value="complete">Complete Linkage</option>\n+\t\t<option value="single">Single Linkage</option>\n+\t\t<option value="ward" selected="true">Ward</option>\n+\t\t<option value="mcquitty">Mcquitty</option>\t \n+\t\t<option value="median">Median</option>\t \n+\t\t<option value="centroid">Centroid</option>\t \n+\t</param>\n+ <param name="rowDendroCut" type="select" label="Create row categorical covariate bar based on number of top-level dendrogram clusters" >\n+ \t\t<option value="0" selected="true" >None</option>\n+ \t\t<option value="2" >2</option>\n+ \t\t<option value="3" >3</option>\n+ \t\t<option value="4" >4</option>\n+ \t\t<option value="5" >5</option>\n+ \t\t<option value="6" >6</option>\n+ \t\t<option value="7" >7</option>\n+ \t\t<option value="8" >8</option>\n+ \t\t<option value="9" >9</option>\n+ \t\t<option value="10" >10</option>\n+ </param>\n+ </when>\n+ <when value="Original">\n+\t\t <param name="rowDistanceMeasure" type="text" size="0" value="n/a"/>\n+\t\t <param name="rowAgglomerationMethod" type="text" size="0" value="n/a"/>\n+\t\t <param name="rowDendroCut" size="0" type="text" value="0"/>\n+ </when>\n+ <when value="Random">\n+\t\t <param name="rowDistanceMeasure" type="text" size="0" value="n/a"/>\n+\t\t <param name="rowAgglomerationMethod" type="text" size="0" value="n/a"/>\n+\t\t <param name="rowDe'..b'+ \t\t<option value="8" >8</option>\n+ \t\t<option value="9" >9</option>\n+ \t\t<option value="10" >10</option>\n+ </param>\n+ </when>\n+ <when value="Original">\n+\t\t <param name="columnDistanceMeasure" type="text" size="0" value="n/a"/>\n+\t\t <param name="columnAgglomerationMethod" type="text" size="0" value="n/a"/>\n+\t\t <param name="colDendroCut" type="text" size="0" value="0"/>\n+ </when>\n+ <when value="Random">\n+\t\t <param name="columnDistanceMeasure" type="text" size="0" value="n/a"/>\n+\t\t <param name="columnAgglomerationMethod" type="text" size="0" value="n/a"/>\n+\t\t <param name="colDendroCut" type="text" size="0" value="0"/>\n+ </when>\n+ </conditional>\n+ <param name="colDataType" type="select" label="Linkouts to column data type info" >\n+ <option value="labels" selected="true" >None</option>\n+ <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>\n+ <option value="bio.feature.agilent" >Agilent Id</option>\n+ <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>\n+ <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>\n+ <option value="bio.gene.entrez" >Gene Entrez Id</option>\n+ <option value="bio.gene.hugo" >Gene HUGO symbol</option>\n+ <option value="bio.go" >Gene Ontology (GO) Id</option>\n+ <option value="bio.geo.acc" >GEO Accession Id</option>\n+ <option value="bio.probe.illumina" >Illumina Probe Id</option>\n+ <option value="bio.probe.infinium" >Infinium Probe Id</option>\n+ <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>\n+ <option value="bio.mirna" >miRNA Id</option>\n+ <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>\n+ <option value="bio.pubmed" >Pubmed Id</option>\n+ <option value="bio.pubmed.search" >Pubmed Search Term</option>\n+ <option value="scholar" >Scholarly term</option>\n+ <option value="bio.gene.unigene" >Unigene CId</option>\n+ <option value="bio.protein.uniprot" >UniProt Id</option>\n+ </param> \n+ <repeat name="operations" title="Covariate Bars">\n+ <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name">\n+ <sanitizer invalid_char="_">\n+ <valid initial="none">\n+ <add preset="string.letters"/>\n+ <add preset="string.digits"/>\n+ </valid>\n+ <mapping initial="none">\n+ </mapping>\n+ </sanitizer>\n+ </param>\n+ <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/>\n+\t<param name="cat" type="select" label="Axis Covariate Type">\n+\t <option value="row_categorical" >row categorical</option>\n+\t <option value="row_continuous" >row continuous</option>\n+\t <option value="column_categorical" >column categorical</option>\n+\t <option value="column_continuous" >column continuous</option>\n+\t</param>\n+ </repeat> \n+ </inputs>\n+ <outputs>\n+ <data name="output" label=\'${hmname}\' format="ngchm"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="inputmatrix" value="400x400.txt" />\n+ <param name="hmname" value="testRun" />\n+ <param name="$hmdesc" value="validateTool" />\n+ <param name="summarymethod" value="average" />\n+ <param name="rowOrderMethod" value="Hierarchical" />\n+ <param name="rowDistanceMeasure" value="manhattan" />\n+ <param name="rowAgglomerationMethod" value="ward" />\n+ <param name="columnOrderMethod" value="Hierarchical" />\n+ <param name="columnDistanceMeasure" value="manhattan" />\n+ <param name="columnAgglomerationMethod" value="ward" />\n+ <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" /> \n+\n+ </test>\n+<!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->\n+ </tests>\n+ </tool>\n' |