Mercurial > repos > md-anderson-bioinformatics > heat_map_creation
annotate mda_heatmap_gen.xml @ 36:11a5827d5559 draft
Uploaded
| author | insilico-bob |
|---|---|
| date | Tue, 06 Nov 2018 16:29:17 -0500 |
| parents | 6ad3c487987d |
| children | f2272e907f1b |
| rev | line source |
|---|---|
| 13 | 1 <?xml version="1.0" encoding="UTF-8" ?> |
| 36 | 2 <tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.3"> |
| 34 | 3 <requirements> |
| 36 | 4 <requirement type="package" version="3.4.1">r-base</requirement> |
| 5 <requirement type="package" version="8.0.144">openjdk</requirement> | |
| 34 | 6 </requirements> |
| 7 <description>Create Clustered Heat Maps</description> | |
| 8 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh "standard" "Heat_Map_$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__/' 0 0 labels labels 'None' | |
| 13 | 9 #for $op in $operations |
|
35
6ad3c487987d
Uploaded ng-chm version 2.5.3 handles java 8 issue and updates to heatmap viewer
insilico-bob
parents:
34
diff
changeset
|
10 '${op.class_name}' |
|
6ad3c487987d
Uploaded ng-chm version 2.5.3 handles java 8 issue and updates to heatmap viewer
insilico-bob
parents:
34
diff
changeset
|
11 '${op.repeatinput.file_name}' |
|
6ad3c487987d
Uploaded ng-chm version 2.5.3 handles java 8 issue and updates to heatmap viewer
insilico-bob
parents:
34
diff
changeset
|
12 '${op.cat}' |
| 13 | 13 #end for |
| 14 '$output' | |
| 15 </command> | |
| 16 <stdio> | |
| 17 <exit_code range="1:" level="fatal" /> | |
| 18 </stdio> | |
| 19 <inputs> | |
| 33 | 20 <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data." /> |
| 34 | 21 <param name="hmname" size="40" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/> |
| 22 <sanitizer> | |
| 23 <valid> | |
| 24 <add preset="string.printable"/> | |
| 25 <!-- <add value="string.letters"/> | |
| 26 <add value="string.digits"/> | |
| 27 <add value="-"/> | |
| 28 <add value="_"/> | |
| 29 --> | |
| 30 <remove value="""/> | |
| 31 <remove value="'"/> | |
| 32 <remove value=" "/> | |
| 33 </valid> | |
| 34 </sanitizer> | |
| 33 | 35 <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."/> |
| 34 | 36 <sanitizer> |
| 37 <valid> | |
| 38 <add preset="string.printable"/> | |
| 39 <add value="string.letters"/> | |
| 40 <add value="string.digits"/> | |
| 41 <add value="-"/> | |
| 42 <add value="_"/> | |
| 43 <remove value="""/> | |
| 44 <remove value="'"/> | |
| 45 <remove value=" "/> | |
| 46 </valid> | |
| 47 </sanitizer> | |
| 33 | 48 <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."> |
| 32 | 49 <option value="average">Average</option> |
| 50 <option value="sample">Sample</option> | |
| 51 <option value="mode">Mode</option> | |
| 13 | 52 </param> |
| 33 | 53 <conditional name="d_rows"> |
| 54 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Determine if rows should be clustered, randomized, or remain as is."> | |
| 13 | 55 <option value="Hierarchical">Hierarchical Clustering</option> |
| 56 <option value="Original">Original Order</option> | |
| 57 <option value="Random">Random</option> | |
| 58 </param> | |
| 59 <when value="Hierarchical"> | |
| 33 | 60 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="For clustering, select the method of determining distance between rows"> |
| 32 | 61 <option value="euclidean">Euclidean</option> |
| 62 <option value="binary">Binary</option> | |
| 63 <option value="manhattan">Manhattan</option> | |
| 64 <option value="maximum">Maximum</option> | |
| 65 <option value="canberra">Canberra</option> | |
| 66 <option value="minkowski">Minkowski</option> | |
| 67 <option value="correlation">Correlation</option> | |
| 68 </param> | |
| 33 | 69 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="For clustering, select algorithm for building clusters."> |
| 32 | 70 <option value="average">Average Linkage</option> |
| 71 <option value="complete">Complete Linkage</option> | |
| 72 <option value="single">Single Linkage</option> | |
| 73 <option value="ward" selected="true">Ward</option> | |
| 74 <option value="mcquitty">Mcquitty</option> | |
| 75 <option value="median">Median</option> | |
| 76 <option value="centroid">Centroid</option> | |
| 77 </param> | |
| 13 | 78 </when> |
| 79 <when value="Original"> | |
| 32 | 80 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> |
| 81 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | |
| 13 | 82 </when> |
| 83 <when value="Random"> | |
| 32 | 84 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> |
| 85 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | |
| 13 | 86 </when> |
| 87 </conditional> | |
| 88 <conditional name="d_cols"> | |
| 33 | 89 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Determine if columns should be clustered, randomized, or remain as is."> |
| 13 | 90 <option value="Hierarchical">Hierarchical Clustering</option> |
| 91 <option value="Original">Original Order</option> | |
| 92 <option value="Random">Random</option> | |
| 93 </param> | |
| 94 <when value="Hierarchical"> | |
| 33 | 95 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="For clustering, select the method of determining distance between columns"> |
| 32 | 96 <option value="euclidean">Euclidean</option> |
| 97 <option value="binary">Binary</option> | |
| 98 <option value="manhattan">Manhattan</option> | |
| 99 <option value="maximum">Maximum</option> | |
| 100 <option value="canberra">Canberra</option> | |
| 101 <option value="minkowski">Minkowski</option> | |
| 102 <option value="correlation">Correlation</option> | |
| 103 </param> | |
| 33 | 104 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="For clustering, select algorithm for building clusters."> |
| 32 | 105 <option value="average">Average Linkage</option> |
| 106 <option value="complete">Complete Linkage</option> | |
| 107 <option value="single">Single Linkage</option> | |
| 108 <option value="ward" selected="true">Ward</option> | |
| 109 <option value="mcquitty">Mcquitty</option> | |
| 110 <option value="median">Median</option> | |
| 111 <option value="centroid">Centroid</option> | |
| 112 </param> | |
| 13 | 113 </when> |
| 114 <when value="Original"> | |
| 32 | 115 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> |
| 116 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | |
| 13 | 117 </when> |
| 118 <when value="Random"> | |
| 32 | 119 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> |
| 120 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | |
| 13 | 121 </when> |
| 122 </conditional> | |
| 123 <repeat name="operations" title="Covariate Bars"> | |
| 34 | 124 <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label."> |
| 125 <sanitizer> | |
| 126 <valid> | |
| 127 <add preset="string.printable"/> | |
| 128 <remove value="""/> | |
| 129 <remove value="'"/> | |
| 130 <remove value=" "/> | |
| 13 | 131 </valid> |
| 132 </sanitizer> | |
| 133 </param> | |
| 34 | 134 <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."/> |
| 33 | 135 <param name="cat" type="select" label="Axis Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values."> |
| 32 | 136 <option value="row_categorical" >Row Categorical</option> |
| 137 <option value="row_continuous" >Row Continuous</option> | |
| 138 <option value="column_categorical" >Column Categorical</option> | |
| 139 <option value="column_continuous" >Column Continuous</option> | |
| 13 | 140 </param> |
| 141 </repeat> | |
| 142 </inputs> | |
| 143 <outputs> | |
| 32 | 144 <data name="output" label='Heat_Map_$hmname' format="ngchm"/> |
| 13 | 145 </outputs> |
| 146 <tests> | |
| 147 <test> | |
| 148 <param name="inputmatrix" value="400x400.txt" /> | |
| 149 <param name="hmname" value="testRun" /> | |
| 150 <param name="$hmdesc" value="validateTool" /> | |
| 32 | 151 <param name="summarymethod" value="Average" /> |
| 13 | 152 <param name="rowOrderMethod" value="Hierarchical" /> |
| 32 | 153 <param name="rowDistanceMeasure" value="Manhattan" /> |
| 154 <param name="rowAgglomerationMethod" value="Ward" /> | |
| 13 | 155 <param name="columnOrderMethod" value="Hierarchical" /> |
| 32 | 156 <param name="columnDistanceMeasure" value="Manhattan" /> |
| 157 <param name="columnAgglomerationMethod" value="Ward" /> | |
| 13 | 158 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" /> |
| 159 | |
| 160 </test> | |
| 161 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied --> | |
| 162 </tests> | |
| 163 </tool> |