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| author | insilico-bob |
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| date | Thu, 20 Jun 2019 11:31:24 -0400 |
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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">$__tool_directory__/heatmap_advanced.sh "$__tool_directory__" "$__tool_data_path__/" "chm_name|Heat_Map_$hmname" "chm_description|$hmdesc" "summary_width|$summaryDisplayWidth" "row_configuration|order_method|${d_rows.rowOrderMethod}|distance_metric|${d_rows.rowDistanceMeasure}|agglomeration_method|${d_rows.rowAgglomerationMethod}|tree_covar_cuts|${d_rows.rowDendroCut}|data_type|$rowDataType|top_items|$rowTopItems|tree_cuts|${d_rows.rcutrows.rowDendroTreeCut}|${d_rows.rcutrows.raddcuts}|dendro_show|${d_rows.rowDendroShow}|dendro_height|${d_rows.rowDendroHeight}" "col_configuration|order_method|${d_cols.columnOrderMethod}|distance_metric|${d_cols.columnDistanceMeasure}|agglomeration_method|${d_cols.columnAgglomerationMethod}|tree_covar_cuts|${d_cols.colDendroCut}|data_type|$colDataType|top_items|$colTopItems|tree_cuts|${d_cols.ccutrows.colDendroTreeCut}|${d_cols.ccutrows.caddcuts}|dendro_show|${d_cols.columnDendroShow}|dendro_height|${d_cols.columnDendroHeight}" #for $attr in $hm_attribute 'attribute|${attr.attrbute_key}':'${attr.attrbute_value}' #end for #for $mx in $matrices 'matrix_files|path|$mx.dataLayer|name|${mx.dataLayerName}|summary_method|${mx.summarymethod}|selection_color|${mx.dataLayerSelectionColor}|cuts_color|${mx.dataLayerCutsColor}|grid_color|${mx.dataLayerGridColor}|grid_show|${mx.dataLayerGridShow}|${mx.colorsBreaks.setColorsBreaks}|${mx.colorsBreaks.matrixColor1}|${mx.colorsBreaks.matrixColor2}|${mx.colorsBreaks.matrixColor3}|${mx.colorsBreaks.matrixBreak1}|${mx.colorsBreaks.matrixBreak2}|${mx.colorsBreaks.matrixBreak3}|${mx.colorsBreaks.missingColor}' #end for #for $op in $operations 'classification|name|${op.class_name}|path|${op.repeatinput.file_name}|category|${op.cattype.cat}|bar_type|${op.cattype.scatbar.bartype}|height|${op.classHeight}|fg_color|${op.cattype.scatbar.fg_color}|bg_color|${op.cattype.scatbar.bg_color}' #end for 'output_location|$output' </command> <stdio> <exit_code range="1:" level="fatal" /> </stdio> <inputs> <repeat name="matrices" title="Heat Map Matrices"> <param name="dataLayer" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data."/> <param name="dataLayerName" size="40" type="text" value="Data_Layer_name" label="Data Layer Name" help="Name for data layer (no spaces)."> <sanitizer> <valid> <add preset="string.printable"/> <remove value="""/> <remove value="'"/> <remove value=" "/> </valid> </sanitizer> </param> <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="colorsBreaks"> <param name="setColorsBreaks" type="select" label="Colors and Breakpoints" help="Select whether to set your own colors and breakpoints or use default values."> <option value="none">Use System Generated Colors and Breakpoints</option> <option value="defined">Define Your Own Colors and Breakpoints</option> </param> <when value="none"> <param name="matrixColor1" type="text" size="0" hidden="true" value="0"/> <param name="matrixBreak1" type="text" size="0" hidden="true" value="0"/> <param name="matrixColor2" type="text" size="0" hidden="true" value="0"/> <param name="matrixBreak2" type="text" size="0" hidden="true" value="0"/> <param name="matrixColor3" type="text" size="0" hidden="true" value="0"/> <param name="matrixBreak3" type="text" size="0" hidden="true" value="0"/> <param name="missingColor" type="text" size="0" hidden="true" value="0"/> </when> <when value="defined"> <param name="matrixColor1" type="color" label="Color for Breakpoint One" value="#ff0000"/> <param name="matrixBreak1" type="text" label="Value for Breakpoint One" value="-1"/> <param name="matrixColor2" type="color" label="Color for Breakpoint Two" value="#ffffff"/> <param name="matrixBreak2" type="text" label="Value for Breakpoint Two" value="0"/> <param name="matrixColor3" type="color" label="Color for Breakpoint Three" value="#0000ff"/> <param name="matrixBreak3" type="text" label="Value for Breakpoint Three" value="1"/> <param name="missingColor" type="color" label="Color for Missing Values" value="#000000"/> </when> </conditional> <param name="dataLayerSelectionColor" type="color" label="Color for selection box" value="#00ff38"/> <param name="dataLayerCutsColor" type="color" label="Color for Heat Map Gaps" value="#ffffff"/> <param name="dataLayerGridColor" type="color" label="Color for Heat Map Grid" value="#ffffff"/> <param name="dataLayerGridShow" type="select" label="Show Heat Map Grid"> <option value="Y">Yes</option> <option value="N">No</option> </param> </repeat> <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="summaryDisplayWidth" type="select" label="Summary Display Width %" help="Sets the percentage of the viewer display of the summary panel."> <option value="50">50%</option> <option value="10">10%</option> <option value="20">20%</option> <option value="30">30%</option> <option value="40">40%</option> <option value="60">60%</option> <option value="70">70%</option> <option value="80">80%</option> <option value="90">90%</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> ** breaks dendrogram --> <option value="manhattan">Manhattan</option> <option value="maximum">Maximum</option> <!-- <option value="canberra">Canberra</option> ** breaks dendrogram --> <option value="minkowski">Minkowski</option> <!-- <option value="correlation">Correlation</option> ** breaks dendrogram --> </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> ** breaks dendrogram <option value="centroid">Centroid</option> ** breaks dendrogram --> </param> <param name="rowDendroShow" type="select" label="Show Row Dendrogram" help="For setting the visibility of the row dendrogram."> <option value="ALL">Summary and Detail</option> <option value="SUMMARY">Summary Only</option> <option value="NONE">Hide</option> </param> <param name="rowDendroHeight" type="select" label="Row Dendrogram Display Height" help="For adjusting the displayed height of the dendrogram bar."> <option value="100">100%</option> <option value="50">50%</option> <option value="75">75%</option> <option value="125">125%</option> <option value="150">150%</option> <option value="200">200%</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="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="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> ** breaks dendrogram --> <option value="manhattan">Manhattan</option> <option value="maximum">Maximum</option> <!-- <option value="canberra">Canberra</option> ** breaks dendrogram --> <option value="minkowski">Minkowski</option> <!-- <option value="correlation">Correlation</option> ** breaks dendrogram --> </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> ** breaks dendrogram <option value="centroid">Centroid</option> ** breaks dendrogram --> </param> <param name="columnDendroShow" type="select" label="Show Column Dendrogram" help="For setting the visibility of the column dendrogram."> <option value="ALL">Summary and Detail</option> <option value="SUMMARY">Summary Only</option> <option value="NONE">Hide</option> </param> <param name="columnDendroHeight" type="select" label="Column Dendrogram Display Height" help="For adjusting the displayed height of the dendrogram bar."> <option value="100">100%</option> <option value="50">50%</option> <option value="75">75%</option> <option value="125">125%</option> <option value="150">150%</option> <option value="200">200%</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="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="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."/> <param name="classHeight" size="10" type="text" value="15" label="Covariate Display Height" help="Set the display height for column covariates and width for row covariates."/> <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_discrete" >Row Categorical</option> <option value="row_continuous" >Row Continuous</option> <option value="column_discrete" >Column Categorical</option> <option value="column_continuous" >Column Continuous</option> </param> <when value="row_continuous"> <conditional name="scatbar"> <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 value="color_plot"> <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/> <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/> </when> <when value="bar_plot"> <param name="bg_color" type="color" label="Color for Bar Plot Background" value="#ffffff"/> <param name="fg_color" type="color" label="Color for Bar Plot Foreground" value="#000000"/> </when> <when value="scatter_plot"> <param name="bg_color" type="color" label="Color for Scatter Plot Background" value="#ffffff"/> <param name="fg_color" type="color" label="Color for Scatter Plot Foreground" value="#000000"/> </when> </conditional> </when> <when value="column_continuous"> <conditional name="scatbar"> <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 value="color_plot"> <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/> <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/> </when> <when value="bar_plot"> <param name="bg_color" type="color" label="Color for Bar Plot Background" value="#ffffff"/> <param name="fg_color" type="color" label="Color for Bar Plot Foreground" value="#000000"/> </when> <when value="scatter_plot"> <param name="bg_color" type="color" label="Color for Scatter Plot Background" value="#ffffff"/> <param name="fg_color" type="color" label="Color for Scatter Plot Foreground" value="#000000"/> </when> </conditional> </when> <when value="column_discrete"> <conditional name="scatbar"> <param name="bartype" type="select" hidden="true"> <option value="color_plot" >Standard</option> </param> <when value="color_plot"> <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/> <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/> </when> </conditional> </when> <when value="row_discrete"> <conditional name="scatbar"> <param name="bartype" type="select" hidden="true"> <option value="color_plot" >Standard</option> </param> <when value="color_plot"> <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/> <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/> </when> </conditional> </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>