Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced
comparison mda_advanced_heatmap_gen.xml @ 1:603f99d9e776 draft
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author | insilico-bob |
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date | Tue, 05 Dec 2017 14:59:26 -0500 |
parents | 8893ea2915cc |
children | 19382473a76b |
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0:8893ea2915cc | 1:603f99d9e776 |
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1 <?xml version="1.0" encoding="UTF-8" ?> | 1 <?xml version="1.0" encoding="UTF-8" ?> |
2 <tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.0.5"> | 2 <tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.1.1"> |
3 <description> Create Clustered Heat Maps</description> | 3 <description> Create Clustered Heat Maps</description> |
4 <!-- 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 $colDataType --> | 4 <!-- command interpreter="python" detect_errors="aggressive">$__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 $colDataType --> |
5 <command interpreter="bash" detect_errors="aggressive">$__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 $colDataType | 5 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.sh 'advanced' '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 $colDataType 'c_${d_rows.rcutrows.rowDendroTreeCut}' 'c_${d_cols.ccutrows.colDendroTreeCut}' 't_$rowTopItems' 't_$colTopItems' |
6 | 6 |
7 " | 7 " |
8 #for $attr in $hm_attribute | 8 #for $attr in $hm_attribute |
9 ${attr.attrbute_key}:${attr.attrbute_value}; | 9 ${attr.attrbute_key}:${attr.attrbute_value}; |
10 #end for | 10 #end for |
11 " | 11 " |
12 | 12 |
13 #for $op in $operations | 13 #for $op in $operations |
14 ${op.class_name} | 14 ${op.class_name} |
15 ${op.repeatinput.file_name} | 15 ${op.repeatinput.file_name} |
16 ${op.cat} | 16 ${op.cattype.cat} |
17 ${op.cattype.bartype} | |
17 #end for | 18 #end for |
18 '$output' | 19 '$output' |
19 </command> | 20 </command> |
20 <stdio> | 21 <stdio> |
21 <exit_code range="1:" level="fatal" /> | 22 <exit_code range="1:" level="fatal" /> |
22 </stdio> | 23 </stdio> |
23 <inputs> | 24 <inputs> |
24 <param name="inputmatrix" type="data" format="Tabular" label="Input Matrix" /> | 25 <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data."/> |
25 <param name="hmname" size="20" type="text" value="Heat_Map_name" label="User Defined Heat Map Name"/> | 26 <param name="hmname" size="20" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/> |
26 <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="User Defined Heat Map Description"/> | 27 <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."/> |
27 <param name="summarymethod" type="select" label="Data Summarization Method"> | 28 <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."> |
28 <option value="average">Average</option> | 29 <option value="average">Average</option> |
29 <option value="sample">Sample</option> | 30 <option value="sample">Sample</option> |
30 <option value="mode">Mode</option> | 31 <option value="mode">Mode</option> |
31 </param> | 32 </param> |
32 <conditional name="d_rows"> | 33 <conditional name="d_rows"> |
33 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random"> | 34 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Determine if rows should be clustered, randomized, or remain as is."> |
34 <option value="Hierarchical">Hierarchical Clustering</option> | 35 <option value="Hierarchical">Hierarchical Clustering</option> |
35 <option value="Original">Original Order</option> | 36 <option value="Original">Original Order</option> |
36 <option value="Random">Random</option> | 37 <option value="Random">Random</option> |
37 </param> | 38 </param> |
39 <when value="Hierarchical"> | |
40 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="For clustering, select the method of determining distance between rows."> | |
41 <option value="euclidean">Euclidean</option> | |
42 <option value="binary">Binary</option> | |
43 <option value="manhattan">Manhattan</option> | |
44 <option value="maximum">Maximum</option> | |
45 <option value="canberra">Canberra</option> | |
46 <option value="minkowski">Minkowski</option> | |
47 <option value="correlation">Correlation</option> | |
48 </param> | |
49 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="For clustering, select algorithm for building clusters."> | |
50 <option value="average">Average Linkage</option> | |
51 <option value="complete">Complete Linkage</option> | |
52 <option value="single">Single Linkage</option> | |
53 <option value="ward" selected="true">Ward</option> | |
54 <option value="mcquitty">Mcquitty</option> | |
55 <option value="median">Median</option> | |
56 <option value="centroid">Centroid</option> | |
57 </param> | |
58 <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."> | |
59 <option value="0" selected="true" >None</option> | |
60 <option value="2" >2</option> | |
61 <option value="3" >3</option> | |
62 <option value="4" >4</option> | |
63 <option value="5" >5</option> | |
64 <option value="6" >6</option> | |
65 <option value="7" >7</option> | |
66 <option value="8" >8</option> | |
67 <option value="9" >9</option> | |
68 <option value="10" >10</option> | |
69 </param> | |
70 <conditional name="rcutrows"> | |
71 <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> | |
72 <option value="none">None</option> | |
73 <option value="treecuts">Cluster-Based Gaps</option> | |
74 <option value="positional">Fixed Gaps</option> | |
75 </param> | |
76 <when value="none"> | |
77 <param name="rowDendroTreeCut" type="text" size="0" hidden="true" value="0"/> | |
78 </when> | |
79 <when value="treecuts"> | |
80 <param name="rowDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters." > | |
81 <option value="0t" selected="true" >None</option> | |
82 <option value="2t" >2</option> | |
83 <option value="3t" >3</option> | |
84 <option value="4t" >4</option> | |
85 <option value="5t" >5</option> | |
86 <option value="6t" >6</option> | |
87 <option value="7t" >7</option> | |
88 <option value="8t" >8</option> | |
89 <option value="9t" >9</option> | |
90 <option value="10t" >10</option> | |
91 </param> | |
92 </when> | |
93 <when value="positional"> | |
94 <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."/> | |
95 </when> | |
96 </conditional> | |
97 </when> | |
98 <when value="Original"> | |
99 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> | |
100 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | |
101 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/> | |
102 <conditional name="rcutrows"> | |
103 <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> | |
104 <option value="none">None</option> | |
105 <option value="positional">Fixed Gaps</option> | |
106 </param> | |
107 <when value="none"> | |
108 <param name="rowDendroTreeCut" type="text" size="100" value="None" hidden="true"/> | |
109 </when> | |
110 <when value="positional"> | |
111 <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."/> | |
112 </when> | |
113 </conditional> | |
114 </when> | |
115 <when value="Random"> | |
116 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> | |
117 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | |
118 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/> | |
119 <conditional name="rcutrows"> | |
120 <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> | |
121 <option value="none">None</option> | |
122 <option value="positional">Fixed Gaps</option> | |
123 </param> | |
124 <when value="none"> | |
125 <param name="rowDendroTreeCut" type="text" size="100" value="None" hidden="true"/> | |
126 </when> | |
127 <when value="positional"> | |
128 <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."/> | |
129 </when> | |
130 </conditional> | |
131 </when> | |
132 </conditional> | |
133 <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."/> | |
134 <param name="rowDataType" type="select" label="Row Label Type" help="Enable label driven link-outs by specifying the type of row labels."> | |
135 <option value="labels" selected="true" >None</option> | |
136 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option> | |
137 <option value="bio.feature.agilent" >Agilent Id</option> | |
138 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option> | |
139 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option> | |
140 <option value="bio.gene.entrez" >Gene Entrez Id</option> | |
141 <option value="bio.gene.hugo" >Gene HUGO symbol</option> | |
142 <option value="bio.go" >Gene Ontology (GO) Id</option> | |
143 <option value="bio.geo.acc" >GEO Accession Id</option> | |
144 <option value="bio.probe.illumina" >Illumina Probe Id</option> | |
145 <option value="bio.probe.infinium" >Infinium Probe Id</option> | |
146 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option> | |
147 <option value="bio.mirna" >miRNA Id</option> | |
148 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option> | |
149 <option value="bio.pubmed" >Pubmed Id</option> | |
150 <option value="bio.pubmed.search" >Pubmed Search Term</option> | |
151 <option value="scholar" >Scholarly term</option> | |
152 <option value="bio.gene.unigene" >Unigene CId</option> | |
153 <option value="bio.protein.uniprot" >UniProt Id</option> | |
154 </param> | |
155 <conditional name="d_cols"> | |
156 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Determine if columns should be clustered, randomized, or remain as is."> | |
157 <option value="Hierarchical">Hierarchical Clustering</option> | |
158 <option value="Original">Original Order</option> | |
159 <option value="Random">Random</option> | |
160 </param> | |
38 <when value="Hierarchical"> | 161 <when value="Hierarchical"> |
39 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation"> | 162 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="For clustering, select the method of determining distance between columns."> |
40 <option value="euclidean">Euclidean</option> | 163 <option value="euclidean">Euclidean</option> |
41 <option value="binary">Binary</option> | 164 <option value="binary">Binary</option> |
42 <option value="manhattan">Manhattan</option> | 165 <option value="manhattan">Manhattan</option> |
43 <option value="maximum">Maximum</option> | 166 <option value="maximum">Maximum</option> |
44 <option value="canberra">Canberra</option> | 167 <option value="canberra">Canberra</option> |
45 <option value="minkowski">Minkowski</option> | 168 <option value="minkowski">Minkowski</option> |
46 <option value="correlation">Correlation</option> | 169 <option value="correlation">Correlation</option> |
47 </param> | 170 </param> |
48 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'."> | 171 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="For clustering, select algorithm for building clusters."> |
49 <option value="average">Average Linkage</option> | 172 <option value="average">Average Linkage</option> |
50 <option value="complete">Complete Linkage</option> | 173 <option value="complete">Complete Linkage</option> |
51 <option value="single">Single Linkage</option> | 174 <option value="single">Single Linkage</option> |
52 <option value="ward" selected="true">Ward</option> | 175 <option value="ward" selected="true">Ward</option> |
53 <option value="mcquitty">Mcquitty</option> | 176 <option value="mcquitty">Mcquitty</option> |
54 <option value="median">Median</option> | 177 <option value="median">Median</option> |
55 <option value="centroid">Centroid</option> | 178 <option value="centroid">Centroid</option> |
56 </param> | 179 </param> |
57 <param name="rowDendroCut" type="select" label="Create row categorical covariate bar based on number of top-level dendrogram clusters" > | 180 <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."> |
58 <option value="0" selected="true" >None</option> | 181 <option value="0" selected="true" >None</option> |
59 <option value="2" >2</option> | 182 <option value="2" >2</option> |
60 <option value="3" >3</option> | 183 <option value="3" >3</option> |
61 <option value="4" >4</option> | 184 <option value="4" >4</option> |
62 <option value="5" >5</option> | 185 <option value="5" >5</option> |
64 <option value="7" >7</option> | 187 <option value="7" >7</option> |
65 <option value="8" >8</option> | 188 <option value="8" >8</option> |
66 <option value="9" >9</option> | 189 <option value="9" >9</option> |
67 <option value="10" >10</option> | 190 <option value="10" >10</option> |
68 </param> | 191 </param> |
69 </when> | 192 <conditional name="ccutrows"> |
70 <when value="Original"> | 193 <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> |
71 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> | 194 <option value="none">None</option> |
72 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | 195 <option value="treecuts">Cluster-Based Gaps</option> |
73 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/> | 196 <option value="positional">Fixed Gaps</option> |
74 </when> | 197 </param> |
75 <when value="Random"> | 198 <when value="none"> |
76 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> | 199 <param name="colDendroTreeCut" type="text" size="0" hidden="true" value="0"/> |
77 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | 200 </when> |
78 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/> | 201 <when value="treecuts"> |
79 </when> | 202 <param name="colDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters."> |
80 </conditional> | 203 <option value="0t" selected="true" >None</option> |
81 <param name="rowDataType" type="select" label="Linkouts to row data type info" > | 204 <option value="2t" >2</option> |
82 <option value="labels" selected="true" >None</option> | 205 <option value="3t" >3</option> |
83 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option> | 206 <option value="4t" >4</option> |
84 <option value="bio.cbioportal.sampleid" >cBioPortal sample Id</option> | 207 <option value="5t" >5</option> |
85 <option value="bio.gene.entrez" >Gene Entrez Id</option> | 208 <option value="6t" >6</option> |
86 <option value="bio.gene.hugo" >Gene HUGO symbol</option> | 209 <option value="7t" >7</option> |
87 <option value="bio.go" >Gene Ontology (GO) Id</option> | 210 <option value="8t" >8</option> |
88 <option value="bio.geo.acc" >GEO Accession Id</option> | 211 <option value="9t" >9</option> |
89 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option> | 212 <option value="10t" >10</option> |
90 <option value="bio.mirna" >miRNA Id</option> | 213 </param> |
91 <option value="bio.pubmed.search" >Pubmed Search Term</option> | 214 </when> |
92 <option value="scholar" >Scholarly term</option> | 215 <when value="positional"> |
93 <option value="bio.protein.uniprotid" >UniProt Id</option> | 216 <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."/> |
94 </param> | 217 </when> |
95 <conditional name="d_cols"> | 218 </conditional> |
96 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random"> | |
97 <option value="Hierarchical">Hierarchical Clustering</option> | |
98 <option value="Original">Original Order</option> | |
99 <option value="Random">Random</option> | |
100 </param> | |
101 <when value="Hierarchical"> | |
102 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation"> | |
103 <option value="euclidean">Euclidean</option> | |
104 <option value="binary">Binary</option> | |
105 <option value="manhattan">Manhattan</option> | |
106 <option value="maximum">Maximum</option> | |
107 <option value="canberra">Canberra</option> | |
108 <option value="minkowski">Minkowski</option> | |
109 <option value="correlation">Correlation</option> | |
110 </param> | |
111 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'."> | |
112 <option value="average">Average Linkage</option> | |
113 <option value="complete">Complete Linkage</option> | |
114 <option value="single">Single Linkage</option> | |
115 <option value="ward" selected="true">Ward</option> | |
116 <option value="mcquitty">Mcquitty</option> | |
117 <option value="median">Median</option> | |
118 <option value="centroid">Centroid</option> | |
119 </param> | |
120 <param name="colDendroCut" type="select" label="Create column categorical covariate bar based on number of top-level dendrogram clusters" > | |
121 <option value="0" selected="true" >None</option> | |
122 <option value="2" >2</option> | |
123 <option value="3" >3</option> | |
124 <option value="4" >4</option> | |
125 <option value="5" >5</option> | |
126 <option value="6" >6</option> | |
127 <option value="7" >7</option> | |
128 <option value="8" >8</option> | |
129 <option value="9" >9</option> | |
130 <option value="10" >10</option> | |
131 </param> | |
132 </when> | 219 </when> |
133 <when value="Original"> | 220 <when value="Original"> |
134 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> | 221 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> |
135 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | 222 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> |
136 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/> | 223 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/> |
137 </when> | 224 <conditional name="ccutrows"> |
225 <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> | |
226 <option value="none">None</option> | |
227 <option value="positional">Fixed Gaps</option> | |
228 </param> | |
229 <when value="none"> | |
230 <param name="colDendroTreeCut" type="text" size="100" value="None" hidden="true"/> | |
231 </when> | |
232 <when value="positional"> | |
233 <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."/> | |
234 </when> | |
235 </conditional> | |
236 </when> | |
138 <when value="Random"> | 237 <when value="Random"> |
139 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> | 238 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> |
140 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | 239 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> |
141 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/> | 240 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/> |
241 <conditional name="ccutrows"> | |
242 <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> | |
243 <option value="none">None</option> | |
244 <option value="positional">Fixed Gaps</option> | |
245 </param> | |
246 <when value="none"> | |
247 <param name="colDendroTreeCut" type="text" size="100" value="None" hidden="true"/> | |
248 </when> | |
249 <when value="positional"> | |
250 <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."/> | |
251 </when> | |
252 </conditional> | |
142 </when> | 253 </when> |
143 </conditional> | 254 </conditional> |
144 <param name="colDataType" type="select" label="Linkouts to column data type info" > | 255 <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."/> |
256 <param name="colDataType" type="select" label="Column Label Type" help="Enable label driven link-outs by specifying the type of column labels."> | |
145 <option value="labels" selected="true" >None</option> | 257 <option value="labels" selected="true" >None</option> |
146 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option> | 258 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option> |
147 <option value="bio.cbioportal.sampleid" >cBioPortal sample Id</option> | 259 <option value="bio.feature.agilent" >Agilent Id</option> |
260 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option> | |
261 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option> | |
148 <option value="bio.gene.entrez" >Gene Entrez Id</option> | 262 <option value="bio.gene.entrez" >Gene Entrez Id</option> |
149 <option value="bio.gene.hugo" >Gene HUGO symbol</option> | 263 <option value="bio.gene.hugo" >Gene HUGO symbol</option> |
150 <option value="bio.go" >Gene Ontology (GO) Id</option> | 264 <option value="bio.go" >Gene Ontology (GO) Id</option> |
151 <option value="bio.geo.acc" >GEO Accession Id</option> | 265 <option value="bio.geo.acc" >GEO Accession Id</option> |
266 <option value="bio.probe.illumina" >Illumina Probe Id</option> | |
267 <option value="bio.probe.infinium" >Infinium Probe Id</option> | |
152 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option> | 268 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option> |
153 <option value="bio.mirna" >miRNA Id</option> | 269 <option value="bio.mirna" >miRNA Id</option> |
270 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option> | |
271 <option value="bio.pubmed" >Pubmed Id</option> | |
154 <option value="bio.pubmed.search" >Pubmed Search Term</option> | 272 <option value="bio.pubmed.search" >Pubmed Search Term</option> |
155 <option value="scholar" >Scholarly term</option> | 273 <option value="scholar" >Scholarly term</option> |
156 <option value="bio.protein.uniprotid" >UniProt Id</option> | 274 <option value="bio.gene.unigene" >Unigene CId</option> |
275 <option value="bio.protein.uniprot" >UniProt Id</option> | |
157 </param> | 276 </param> |
158 <repeat name="operations" title="Covariate Bars"> | 277 <repeat name="operations" title="Covariate Bars"> |
159 <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name"> | 278 <param name="class_name" size="20" type="text" value="" label="Covariate Name" help="Label for the covariate to display in the heat map."> |
160 <sanitizer invalid_char="_"> | 279 <sanitizer invalid_char="_"> |
161 <valid initial="none"> | 280 <valid initial="none"> |
162 <add preset="string.letters"/> | 281 <add preset="string.letters"/> |
163 <add preset="string.digits"/> | 282 <add preset="string.digits"/> |
164 </valid> | 283 </valid> |
165 <mapping initial="none"> | 284 <mapping initial="none"> |
166 </mapping> | 285 </mapping> |
167 </sanitizer> | 286 </sanitizer> |
168 </param> | 287 </param> |
169 <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/> | 288 <param name="repeatinput" type="data" format="text" label="Covariate File" help="Tab delimited text file with row or column label and covariate value on each line."/> |
170 <param name="cat" type="select" label="Axis Covariate Type"> | 289 <conditional name="cattype"> |
171 <option value="row_categorical" >Row Categorical</option> | 290 <param name="cat" type="select" label="Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values."> |
172 <option value="row_continuous" >Row Continuous</option> | 291 <option value="row_categorical" >Row Categorical</option> |
173 <option value="column_categorical" >Column Categorical</option> | 292 <option value="row_continuous" >Row Continuous</option> |
174 <option value="column_continuous" >Column Continuous</option> | 293 <option value="column_categorical" >Column Categorical</option> |
175 </param> | 294 <option value="column_continuous" >Column Continuous</option> |
176 </repeat> | 295 </param> |
296 <when value="row_continuous"> | |
297 <param name="bartype" type="select" label="Display Type"> | |
298 <option value="color_plot" >Standard</option> | |
299 <option value="bar_plot" >Bar Plot</option> | |
300 <option value="scatter_plot" >Scatter Plot</option> | |
301 </param> | |
302 </when> | |
303 <when value="column_continuous"> | |
304 <param name="bartype" type="select" label="Display Type"> | |
305 <option value="color_plot" >Standard</option> | |
306 <option value="bar_plot" >Bar Plot</option> | |
307 <option value="scatter_plot" >Scatter Plot</option> | |
308 </param> | |
309 </when> | |
310 <when value="column_categorical"> | |
311 <param name="bartype" type="text" hidden="true" value="color_plot"/> | |
312 </when> | |
313 <when value="row_categorical"> | |
314 <param name="bartype" type="text" hidden="true" value="color_plot"/> | |
315 </when> | |
316 </conditional> | |
317 </repeat> | |
177 <repeat name="hm_attribute" title="Heat Map Attributes"> | 318 <repeat name="hm_attribute" title="Heat Map Attributes"> |
178 <param name="attrbute_key" size="50" type="text" value="" label="Heat Map Attributes json pair-- key "> | 319 <param name="attrbute_key" size="50" type="text" value="" label="Heat Map Attribute Key" help="For map level attributes. Enter the key (no spaces)."> |
179 <sanitizer invalid_char="_"> | 320 <sanitizer invalid_char="_"> |
180 <valid initial=""> | 321 <valid initial=""> |
181 <add preset="string.letters"/> | 322 <add preset="string.letters"/> |
182 <add preset="string.digits"/> | 323 <add preset="string.digits"/> |
183 </valid> | 324 </valid> |
184 <mapping initial=""> | 325 <mapping initial=""> |
185 </mapping> | 326 </mapping> |
186 </sanitizer> | 327 </sanitizer> |
187 </param> | 328 </param> |
188 <param name="attrbute_value" size="50" type="text" label="Heat Map Attributes json pairs -- value "> | 329 <param name="attrbute_value" size="50" type="text" label="Heat Map Attributes Value" help="For map level attributes. Enter the value (no spaces)."> |
189 <sanitizer invalid_char="_"> | 330 <sanitizer invalid_char="_"> |
190 <valid initial=""> | 331 <valid initial=""> |
191 <add preset="string.letters"/> | 332 <add preset="string.letters"/> |
192 <add preset="string.digits"/> | 333 <add preset="string.digits"/> |
193 </valid> | 334 </valid> |