Mercurial > repos > peter-waltman > ucsc_cluster_tools2

comparison cluster.tools/partition.xml @ 8:a58527c632b7 draft

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author peter-waltman
date Mon, 11 Mar 2013 16:31:29 -0400
parents 0decf3fd54bc
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7:2efa1a284546 8:a58527c632b7
4 ${dist_obj} 4 ${dist_obj}
5 -n ${direction} 5 -n ${direction}
6 -a $alg_cond.algorithm 6 -a $alg_cond.algorithm
7 #if $alg_cond.algorithm == 'pam' # -m ${alg_cond.distance_metric} 7 #if $alg_cond.algorithm == 'pam' # -m ${alg_cond.distance_metric}
8 #end if 8 #end if
9
10 #if str($numk) != "-1":
9 -k ${numk} 11 -k ${numk}
10 -o ${output} 12 #end if
13
14 #if str($direction) == "rows":
15 -o ${rdata_output_rows}
16 #end if
17
18 #if str($direction) == "cols":
19 -o ${rdata_output_cols}
20 #end if
21
11 22
12 </command> 23 </command>
13 <inputs> 24 <inputs>
14 <param name="dataset" type="data" format='tabular' label="Data Set" help="Specify the data matrix (tab-delimited) to be clustered"/> 25 <param name="dataset" type="data" format='tabular' label="Data Set" help="Specify the data matrix (tab-delimited) to be clustered"/>
15 <param name="dist_obj" type="boolean" label="Distance Object (R dist object)?" truevalue="-D" falsevalue="" checked="False" help="Check if the matrix contains the pairwise distances between a set of objects"/> 26 <param name="dist_obj" type="boolean" label="Distance Object (R dist object)?" truevalue="-D" falsevalue="" checked="False" help="Check if the matrix contains the pairwise distances between a set of objects"/>
38 <option value="canberra">Canberra</option> 49 <option value="canberra">Canberra</option>
39 <option value="binary">Binary</option> 50 <option value="binary">Binary</option>
40 </param> 51 </param>
41 </when> 52 </when>
42 </conditional> 53 </conditional>
43 <param name="numk" type="integer" label="Number of Clusters" value="50" help="Specify the number of clusters to use"/> 54 <param name="numk" type="integer" label="Number of Clusters" value="-1" help="Specify the number of clusters to use (-1 to use default. See help below)."/>
44 55
45 </inputs> 56 </inputs>
46 <outputs> 57 <outputs>
47 <data format="rdata" name="output" label="Partition Clustering Data (RData)"/> 58 <data format="rdata" name="rdata_output_rows" label="Partition Clustering Results; Gene Clusters (RData)">
59 <filter>(direction)=="rows"</filter>
60 </data>
61 <data format="rdata" name="rdata_output_cols" label="Partition Clustering Results; Sample Clusters (RData)">
62 <filter>(direction)=="cols"</filter>
63 </data>
48 </outputs> 64 </outputs>
49 <help> 65 <help>
50 .. class:: infomark 66 .. class:: infomark
51 67
52 **Perform Partition Clustering (Cluster Samples) on a specified data set** 68 **Perform Partition Clustering (Cluster Samples) on a specified data set**
85 * Manhattan (AKA city block) 101 * Manhattan (AKA city block)
86 * Canberra 102 * Canberra
87 * Binary 103 * Binary
88 104
89 105
90 - **Number of Clusters** Specify the number of clusters to use 106 - **Number of Clusters** Specify the number of clusters to use. If set to -1, default values will be used, with the default set as follows:
107 * if samples/columns are being clustered, the **default** is 5.
108 * if genes/rows are being clustered, the **default** is set to num_rows/30, e.g. if there are 600 row/genes in the matrix, the default will be 20 clusters.
91 109
92 </help> 110 </help>
93 </tool> 111 </tool>