Mercurial > repos > xuebing > sharplabtool
comparison tools/new_operations/cluster.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="gops_cluster_1" name="Cluster"> | |
2 <description>the intervals of a dataset</description> | |
3 <command interpreter="python">gops_cluster.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -d $distance -m $minregions -o $returntype</command> | |
4 <inputs> | |
5 <param format="interval" name="input1" type="data"> | |
6 <label>Cluster intervals of</label> | |
7 </param> | |
8 <param name="distance" size="5" type="integer" value="1" help="(bp)"> | |
9 <label>max distance between intervals</label> | |
10 </param> | |
11 <param name="minregions" size="5" type="integer" value="2"> | |
12 <label>min number of intervals per cluster</label> | |
13 </param> | |
14 <param name="returntype" type="select" label="Return type"> | |
15 <option value="1">Merge clusters into single intervals</option> | |
16 <option value="2">Find cluster intervals; preserve comments and order</option> | |
17 <option value="3">Find cluster intervals; output grouped by clusters</option> | |
18 <option value="4">Find the smallest interval in each cluster</option> | |
19 <option value="5">Find the largest interval in each cluster</option> | |
20 </param> | |
21 </inputs> | |
22 <outputs> | |
23 <data format="input" name="output" metadata_source="input1" /> | |
24 </outputs> | |
25 <code file="operation_filter.py"> | |
26 <hook exec_after_process="exec_after_cluster" /> | |
27 </code> | |
28 <tests> | |
29 <test> | |
30 <param name="input1" value="5.bed" /> | |
31 <param name="distance" value="1" /> | |
32 <param name="minregions" value="2" /> | |
33 <param name="returntype" value="1" /> | |
34 <output name="output" file="gops-cluster-1.bed" /> | |
35 </test> | |
36 <test> | |
37 <param name="input1" value="gops_cluster_bigint.bed" /> | |
38 <param name="distance" value="1" /> | |
39 <param name="minregions" value="2" /> | |
40 <param name="returntype" value="1" /> | |
41 <output name="output" file="gops-cluster-1.bed" /> | |
42 </test> | |
43 <test> | |
44 <param name="input1" value="5.bed" /> | |
45 <param name="distance" value="1" /> | |
46 <param name="minregions" value="2" /> | |
47 <param name="returntype" value="2" /> | |
48 <output name="output" file="gops-cluster-2.bed" /> | |
49 </test> | |
50 <test> | |
51 <param name="input1" value="5.bed" /> | |
52 <param name="distance" value="1" /> | |
53 <param name="minregions" value="2" /> | |
54 <param name="returntype" value="3" /> | |
55 <output name="output" file="gops-cluster-3.bed" /> | |
56 </test> | |
57 </tests> | |
58 <help> | |
59 | |
60 .. class:: infomark | |
61 | |
62 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. | |
63 | |
64 ----- | |
65 | |
66 **Screencasts!** | |
67 | |
68 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). | |
69 | |
70 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations | |
71 | |
72 ----- | |
73 | |
74 **Syntax** | |
75 | |
76 - **Maximum distance** is greatest distance in base pairs allowed between intervals that will be considered "clustered". **Negative** values for distance are allowed, and are useful for clustering intervals that overlap. | |
77 - **Minimum intervals per cluster** allow a threshold to be set on the minimum number of intervals to be considered a cluster. Any area with less than this minimum will not be included in the output. | |
78 - **Merge clusters into single intervals** outputs intervals that span the entire cluster. | |
79 - **Find cluster intervals; preserve comments and order** filters out non-cluster intervals while maintaining the original ordering and comments in the file. | |
80 - **Find cluster intervals; output grouped by clusters** filters out non-cluster intervals, but outputs the cluster intervals so that they are grouped together. Comments and original ordering in the file are lost. | |
81 | |
82 ----- | |
83 | |
84 **Example** | |
85 | |
86 .. image:: ./static/operation_icons/gops_cluster.gif | |
87 | |
88 </help> | |
89 </tool> |