| Previous changeset 11:80ab17e6cc42 (2017-01-26) Next changeset 13:7258044eda47 (2017-01-26) |
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Commit message:
Deleted selected files |
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removed:
mda_heatmap_gen.xml |
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| diff -r 80ab17e6cc42 -r 4202a0cf00a7 mda_heatmap_gen.xml --- a/mda_heatmap_gen.xml Thu Jan 26 10:15:44 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,204 +0,0 @@\n-<?xml version="1.0" encoding="UTF-8" ?>\n-<tool id="mda_heatmap_gen" name="NG-CHM Generator" version="6.0.2">\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' |