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comparison abims_hclustering.xml @ 1:36fc0a87d7fb draft default tip

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author lecorguille
date Fri, 13 Nov 2015 08:43:11 -0500
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0:2f7381ee5235 1:36fc0a87d7fb
1 <tool id="abims_hclustering" name="Hierarchical Clustering" version="1.1"> 1 <tool id="abims_hclustering" name="Hierarchical Clustering" version="1.1.2">
2 2
3 <description>using ctc R package for java-treeview</description> 3 <description>using ctc R package for java-treeview</description>
4 4
5 <command interpreter="Rscript"> 5 <command interpreter="Rscript"><![CDATA[
6 abims_hclustering.r file "$input" method $method link $link keep.hclust FALSE normalization $normalization sep "$sep" dec "$dec" 6 abims_hclustering.r file "$input" method $method link $link keep.hclust FALSE normalization $normalization sep "$sep" dec "$dec" && mv hclust.zip $outputzip
7 </command> 7 ]]></command>
8 8
9 <inputs> 9 <inputs>
10 <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." /> 10 <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
11 <param name="method" type="select" label="Distance measure method" help="the distance measure to be used"> 11 <param name="method" type="select" label="Distance measure method" help="the distance measure to be used">
12 <option value="pearson" selected="true">pearson</option> 12 <option value="pearson" selected="true">pearson</option>
48 <param name="threshold" type="float" label="threshold" value="0.01" help="max adjusted p.value accepted" />--> 48 <param name="threshold" type="float" label="threshold" value="0.01" help="max adjusted p.value accepted" />-->
49 49
50 </inputs> 50 </inputs>
51 51
52 <outputs> 52 <outputs>
53 <data name="hclust_zip" format="zip" from_work_dir="hclust.zip" label="${input.name[:-4]}.hclust.zip" /> 53 <data name="outputzip" format="zip" label="${input.name[:-4]}.heatmap.zip for Java Treeview" />
54 </outputs> 54 </outputs>
55 55
56 <stdio> 56 <stdio>
57 <exit_code range="1:" level="fatal" /> 57 <exit_code range="1:" level="fatal" />
58 </stdio> 58 </stdio>
59 59
60 <help> 60 <help><![CDATA[
61 61
62 62
63 63
64 .. class:: infomark 64 .. class:: infomark
65 65
100 inversions (which are hard to interpret). 100 inversions (which are hard to interpret).
101 101
102 102
103 103
104 104
105 -----------------
106 Workflow position
107 -----------------
108
109
110 **Upstream tools**
111
112 +---------------------------+----------------------------------------+--------+------------------------+
113 | Name | Output file | Format | parameter |
114 +===========================+========================================+========+========================+
115 |xcms.diffreport |xset.diffreport.data_matrix.tsv | Tabular| Data table file |
116 +---------------------------+----------------------------------------+--------+------------------------+
117 |CAMERA.annotateDiffreport |xset.annotatediffreport.data_matrix.tsv | Tabular| Data table file |
118 +---------------------------+----------------------------------------+--------+------------------------+
119 |Anova |xset.anova_filtered.tabular | Tabular| Data table file |
120 +---------------------------+----------------------------------------+--------+------------------------+
121
122
123
124 **Downstream tools**
125
126 +---------------------------+-----------------------------------------------+---------------------+
127 | Name | Output file | Format |
128 +===========================+===============================================+=====================+
129 |Treeview (out of Galaxy) | cdt,gtr and atr files needed for Java Treeview|Java Treeview formats|
130 +---------------------------+-----------------------------------------------+---------------------+
131
132
133
105 ----------- 134 -----------
106 Input files 135 Input files
107 ----------- 136 -----------
108 137
109 +---------------------------+------------+ 138 +---------------------------+------------+
124 The complete linkage method finds similar clusters. The single linkage method (which is closely related to the minimal spanning tree) adopts a ‘friends of friends’ clustering strategy. 153 The complete linkage method finds similar clusters. The single linkage method (which is closely related to the minimal spanning tree) adopts a ‘friends of friends’ clustering strategy.
125 The other methods can be regarded as aiming for clusters with characteristics somewhere between the single and complete link methods. 154 The other methods can be regarded as aiming for clusters with characteristics somewhere between the single and complete link methods.
126 Note however, that methods median and centroid are not leading to a monotone distance measure, or equivalently the resulting dendrograms can have so called inversions (which are hard to interpret). 155 Note however, that methods median and centroid are not leading to a monotone distance measure, or equivalently the resulting dendrograms can have so called inversions (which are hard to interpret).
127 156
128 157
158
129 ------------ 159 ------------
130 Output files 160 Output files
131 ------------ 161 ------------
132 162
133 ***.tab.hclust.zip** 163 ***.tab.hclust.zip**
158 188
159 **>A part of an example of Data Matrix file input** 189 **>A part of an example of Data Matrix file input**
160 190
161 191
162 +--------+------------------+----------------+ 192 +--------+------------------+----------------+
163 | Name | Bur-eH_FSP_102 | Bur-eH_FSP_22 | 193 | Name | Bur-eH_FSP_102 | Bur-eH_FSP_22 |
164 +========+==================+================+ 194 +========+==================+================+
165 |M202T601| 91206595.7559783 |106808979.08546 | 195 |M202T601| 91206595.7559783 |106808979.08546 |
166 +--------+------------------+----------------+ 196 +--------+------------------+----------------+
167 |M234T851| 27249137.275504 |28824971.3177926| 197 |M234T851| 27249137.275504 |28824971.3177926|
168 +--------+------------------+----------------+ 198 +--------+------------------+----------------+
187 .. image:: hclust.png 217 .. image:: hclust.png
188 218
189 219
190 </help> 220 </help>
191 221
192 </tool> 222 ]]></tool>