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comparison mda_advanced_heatmap_gen.xml @ 1:603f99d9e776 draft

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author insilico-bob
date Tue, 05 Dec 2017 14:59:26 -0500
parents 8893ea2915cc
children 19382473a76b
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0:8893ea2915cc 1:603f99d9e776
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>