Mercurial > repos > md-anderson-bioinformatics > heat_map_creation

comparison mda_heatmap_gen.xml @ 32:16593e40c2cd draft

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Version 2.0.5
author insilico-bob
date Thu, 20 Jul 2017 15:31:06 -0400
parents 5d22d515b470
children 0097750ad7ad
comparison
equal deleted inserted replaced
31:e01b833f5d43 32:16593e40c2cd
1 <?xml version="1.0" encoding="UTF-8" ?> 1 <?xml version="1.0" encoding="UTF-8" ?>
2 <tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.0.2"> 2 <tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.0.5">
3 <description>Create Clustered Heat Maps</description> 3 <description>Create Clustered Heat Maps</description>
4 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh '$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType 4 <!-- <command interpreter="python" detect_errors="aggressive">$__tool_directory__/mda_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__' 0 0 labels labels 'None'-->
5 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh "Heat_Map_$hmname" "$hmdesc" '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__/' 0 0 labels labels 'None'
5 #for $op in $operations 6 #for $op in $operations
6 ${op.class_name} 7 ${op.class_name}
7 ${op.repeatinput.file_name} 8 ${op.repeatinput.file_name}
8 ${op.cat} 9 ${op.cat}
9 #end for 10 #end for
11 </command> 12 </command>
12 <stdio> 13 <stdio>
13 <exit_code range="1:" level="fatal" /> 14 <exit_code range="1:" level="fatal" />
14 </stdio> 15 </stdio>
15 <inputs> 16 <inputs>
16 <param name="inputmatrix" type="data" format="text" label="Input Matrix" /> 17 <param name="inputmatrix" type="data" format="Tabular" label="Input Matrix" />
17 <param name="hmname" size="20" type="text" value="Heat_Map_name" label="User Defined Heat Map Name"/> 18 <param name="hmname" size="20" type="text" value="Heat_Map_name" label="User Defined Heat Map Name"/>
18 <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="User Defined Heat Map Description"/> 19 <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="User Defined Heat Map Description"/>
19 <param name="summarymethod" type="select" label="Data Summarization Method"> 20 <param name="summarymethod" type="select" label="Data Summarization Method">
20 <option value="average">average</option> 21 <option value="average">Average</option>
21 <option value="sample">sample</option> 22 <option value="sample">Sample</option>
22 <option value="mode">mode</option> 23 <option value="mode">Mode</option>
23 </param> 24 </param>
24 <conditional name="d_rows"> 25 <conditional name="d_rows">
25 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random"> 26 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">
26 <option value="Hierarchical">Hierarchical Clustering</option> 27 <option value="Hierarchical">Hierarchical Clustering</option>
27 <option value="Original">Original Order</option> 28 <option value="Original">Original Order</option>
28 <option value="Random">Random</option> 29 <option value="Random">Random</option>
29 </param> 30 </param>
30 <when value="Hierarchical"> 31 <when value="Hierarchical">
31 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="euclidean, binary, manhattan, maximum, canberra, minkowski, or correlation"> 32 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation">
32 <option value="euclidean">Euclidean</option> 33 <option value="euclidean">Euclidean</option>
33 <option value="binary">Binary</option> 34 <option value="binary">Binary</option>
34 <option value="manhattan">Manhattan</option> 35 <option value="manhattan">Manhattan</option>
35 <option value="maximum">Maximum</option> 36 <option value="maximum">Maximum</option>
36 <option value="canberra">Canberra</option> 37 <option value="canberra">Canberra</option>
37 <option value="minkowski">Minkowski</option> 38 <option value="minkowski">Minkowski</option>
38 <option value="correlation">Correlation</option> 39 <option value="correlation">Correlation</option>
39 </param> 40 </param>
40 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: 'average' for Average Linkage, 'complete' for Complete Linkage, 'single' for Single Linkage, 'ward', 'mcquitty', 'median', or 'centroid'."> 41 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'.">
41 <option value="average">Average Linkage</option> 42 <option value="average">Average Linkage</option>
42 <option value="complete">Complete Linkage</option> 43 <option value="complete">Complete Linkage</option>
43 <option value="single">Single Linkage</option> 44 <option value="single">Single Linkage</option>
44 <option value="ward" selected="true">Ward</option> 45 <option value="ward" selected="true">Ward</option>
45 <option value="mcquitty">Mcquitty</option> 46 <option value="mcquitty">Mcquitty</option>
46 <option value="median">Median</option> 47 <option value="median">Median</option>
47 <option value="centroid">Centroid</option> 48 <option value="centroid">Centroid</option>
48 </param> 49 </param>
49 <param name="rowDendroCut" type="select" label="Create row categorical covariate bar based on number of top-level dendrogram clusters" >
50 <option value="0" selected="true" >None</option>
51 <option value="2" >2</option>
52 <option value="3" >3</option>
53 <option value="4" >4</option>
54 <option value="5" >5</option>
55 <option value="6" >6</option>
56 <option value="7" >7</option>
57 <option value="8" >8</option>
58 <option value="9" >9</option>
59 <option value="10" >10</option>
60 </param>
61 </when> 50 </when>
62 <when value="Original"> 51 <when value="Original">
63 <param name="rowDistanceMeasure" type="text" size="0" value="n/a"/> 52 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
64 <param name="rowAgglomerationMethod" type="text" size="0" value="n/a"/> 53 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
65 <param name="rowDendroCut" size="0" type="text" value="0"/>
66 </when> 54 </when>
67 <when value="Random"> 55 <when value="Random">
68 <param name="rowDistanceMeasure" type="text" size="0" value="n/a"/> 56 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
69 <param name="rowAgglomerationMethod" type="text" size="0" value="n/a"/> 57 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
70 <param name="rowDendroCut" type="text" size="0" value="0"/>
71 </when> 58 </when>
72 </conditional> 59 </conditional>
73 <param name="rowDataType" type="select" label="Linkouts to row data type info" >
74 <option value="labels" selected="true" >None</option>
75 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
76 <option value="bio.feature.agilent" >Agilent Id</option>
77 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
78 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
79 <option value="bio.gene.entrez" >Gene Entrez Id</option>
80 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
81 <option value="bio.go" >Gene Ontology (GO) Id</option>
82 <option value="bio.geo.acc" >GEO Accession Id</option>
83 <option value="bio.probe.illumina" >Illumina Probe Id</option>
84 <option value="bio.probe.infinium" >Infinium Probe Id</option>
85 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
86 <option value="bio.mirna" >miRNA Id</option>
87 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
88 <option value="bio.pubmed" >Pubmed Id</option>
89 <option value="bio.pubmed.search" >Pubmed Search Term</option>
90 <option value="scholar" >Scholarly term</option>
91 <option value="bio.gene.unigene" >Unigene CID</option>
92 <option value="bio.protein.uniprot" >UniProt Id</option>
93 </param>
94 <conditional name="d_cols"> 60 <conditional name="d_cols">
95 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random"> 61 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">
96 <option value="Hierarchical">Hierarchical Clustering</option> 62 <option value="Hierarchical">Hierarchical Clustering</option>
97 <option value="Original">Original Order</option> 63 <option value="Original">Original Order</option>
98 <option value="Random">Random</option> 64 <option value="Random">Random</option>
99 </param> 65 </param>
100 <when value="Hierarchical"> 66 <when value="Hierarchical">
101 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="euclidean, binary, manhattan, maximum, canberra, minkowski, or correlation"> 67 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation">
102 <option value="euclidean">Euclidean</option> 68 <option value="euclidean">Euclidean</option>
103 <option value="binary">Binary</option> 69 <option value="binary">Binary</option>
104 <option value="manhattan">Manhattan</option> 70 <option value="manhattan">Manhattan</option>
105 <option value="maximum">Maximum</option> 71 <option value="maximum">Maximum</option>
106 <option value="canberra">Canberra</option> 72 <option value="canberra">Canberra</option>
107 <option value="minkowski">Minkowski</option> 73 <option value="minkowski">Minkowski</option>
108 <option value="correlation">Correlation</option> 74 <option value="correlation">Correlation</option>
109 </param> 75 </param>
110 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="Choices: 'average' for Average Linkage, 'complete' for Complete Linkage, 'single' for Single Linkage, 'ward', 'mcquitty', 'median', or 'centroid'."> 76 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'.">
111 <option value="average">Average Linkage</option> 77 <option value="average">Average Linkage</option>
112 <option value="complete">Complete Linkage</option> 78 <option value="complete">Complete Linkage</option>
113 <option value="single">Single Linkage</option> 79 <option value="single">Single Linkage</option>
114 <option value="ward" selected="true">Ward</option> 80 <option value="ward" selected="true">Ward</option>
115 <option value="mcquitty">Mcquitty</option> 81 <option value="mcquitty">Mcquitty</option>
116 <option value="median">Median</option> 82 <option value="median">Median</option>
117 <option value="centroid">Centroid</option> 83 <option value="centroid">Centroid</option>
118 </param> 84 </param>
119 <param name="colDendroCut" type="select" label="Create column categorical covariate bar based on number of top-level dendrogram clusters" >
120 <option value="0" selected="true" >None</option>
121 <option value="2" >2</option>
122 <option value="3" >3</option>
123 <option value="4" >4</option>
124 <option value="5" >5</option>
125 <option value="6" >6</option>
126 <option value="7" >7</option>
127 <option value="8" >8</option>
128 <option value="9" >9</option>
129 <option value="10" >10</option>
130 </param>
131 </when> 85 </when>
132 <when value="Original"> 86 <when value="Original">
133 <param name="columnDistanceMeasure" type="text" size="0" value="n/a"/> 87 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
134 <param name="columnAgglomerationMethod" type="text" size="0" value="n/a"/> 88 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
135 <param name="colDendroCut" type="text" size="0" value="0"/>
136 </when> 89 </when>
137 <when value="Random"> 90 <when value="Random">
138 <param name="columnDistanceMeasure" type="text" size="0" value="n/a"/> 91 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
139 <param name="columnAgglomerationMethod" type="text" size="0" value="n/a"/> 92 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
140 <param name="colDendroCut" type="text" size="0" value="0"/>
141 </when> 93 </when>
142 </conditional> 94 </conditional>
143 <param name="colDataType" type="select" label="Linkouts to column data type info" >
144 <option value="labels" selected="true" >None</option>
145 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
146 <option value="bio.feature.agilent" >Agilent Id</option>
147 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
148 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
149 <option value="bio.gene.entrez" >Gene Entrez Id</option>
150 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
151 <option value="bio.go" >Gene Ontology (GO) Id</option>
152 <option value="bio.geo.acc" >GEO Accession Id</option>
153 <option value="bio.probe.illumina" >Illumina Probe Id</option>
154 <option value="bio.probe.infinium" >Infinium Probe Id</option>
155 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
156 <option value="bio.mirna" >miRNA Id</option>
157 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
158 <option value="bio.pubmed" >Pubmed Id</option>
159 <option value="bio.pubmed.search" >Pubmed Search Term</option>
160 <option value="scholar" >Scholarly term</option>
161 <option value="bio.gene.unigene" >Unigene CId</option>
162 <option value="bio.protein.uniprot" >UniProt Id</option>
163 </param>
164 <repeat name="operations" title="Covariate Bars"> 95 <repeat name="operations" title="Covariate Bars">
165 <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name"> 96 <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name">
166 <sanitizer invalid_char="_"> 97 <sanitizer invalid_char="_">
167 <valid initial="none"> 98 <valid initial="none">
168 <add preset="string.letters"/> 99 <add preset="string.letters"/>
172 </mapping> 103 </mapping>
173 </sanitizer> 104 </sanitizer>
174 </param> 105 </param>
175 <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/> 106 <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/>
176 <param name="cat" type="select" label="Axis Covariate Type"> 107 <param name="cat" type="select" label="Axis Covariate Type">
177 <option value="row_categorical" >row categorical</option> 108 <option value="row_categorical" >Row Categorical</option>
178 <option value="row_continuous" >row continuous</option> 109 <option value="row_continuous" >Row Continuous</option>
179 <option value="column_categorical" >column categorical</option> 110 <option value="column_categorical" >Column Categorical</option>
180 <option value="column_continuous" >column continuous</option> 111 <option value="column_continuous" >Column Continuous</option>
181 </param> 112 </param>
182 </repeat> 113 </repeat>
183 </inputs> 114 </inputs>
184 <outputs> 115 <outputs>
185 <data name="output" label='${hmname}' format="ngchm"/> 116 <data name="output" label='Heat_Map_$hmname' format="ngchm"/>
186 </outputs> 117 </outputs>
187 <tests> 118 <tests>
188 <test> 119 <test>
189 <param name="inputmatrix" value="400x400.txt" /> 120 <param name="inputmatrix" value="400x400.txt" />
190 <param name="hmname" value="testRun" /> 121 <param name="hmname" value="testRun" />
191 <param name="$hmdesc" value="validateTool" /> 122 <param name="$hmdesc" value="validateTool" />
192 <param name="summarymethod" value="average" /> 123 <param name="summarymethod" value="Average" />
193 <param name="rowOrderMethod" value="Hierarchical" /> 124 <param name="rowOrderMethod" value="Hierarchical" />
194 <param name="rowDistanceMeasure" value="manhattan" /> 125 <param name="rowDistanceMeasure" value="Manhattan" />
195 <param name="rowAgglomerationMethod" value="ward" /> 126 <param name="rowAgglomerationMethod" value="Ward" />
196 <param name="columnOrderMethod" value="Hierarchical" /> 127 <param name="columnOrderMethod" value="Hierarchical" />
197 <param name="columnDistanceMeasure" value="manhattan" /> 128 <param name="columnDistanceMeasure" value="Manhattan" />
198 <param name="columnAgglomerationMethod" value="ward" /> 129 <param name="columnAgglomerationMethod" value="Ward" />
199 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" /> 130 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" />
200 131
201 </test> 132 </test>
202 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied --> 133 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->
203 </tests> 134 </tests>