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comparison cluster.xml @ 4:05696474ee89 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:40:19 -0400
parents 765ceb06c3e2
children
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3:765ceb06c3e2 4:05696474ee89
1 <tool id="gops_cluster_1" name="Cluster" version="1.0.0"> 1 <tool id="gops_cluster_1" name="Cluster" version="1.0.0">
2 <description>the intervals of a dataset</description> 2 <description>the intervals of a dataset</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.7.1">bx-python</requirement> 4 <import>macros.xml</import>
5 <requirement type="package" version="1.0.0">galaxy-ops</requirement> 5 </macros>
6 </requirements> 6 <expand macro="requirements" />
7 <trackster_conf/> 7 <code file="operation_filter.py">
8 <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 $returntype</command> 8 <hook exec_after_process="exec_after_cluster" />
9 <inputs> 9 </code>
10 <param format="interval" name="input1" type="data"> 10 <command><![CDATA[
11 <label>Cluster intervals of</label> 11 python '$__tool_directory__/gops_cluster.py'
12 </param> 12 '$input1'
13 <param name="distance" type="integer" value="1" help="(bp)"> 13 '$output'
14 <label>max distance between intervals</label> 14 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
15 </param> 15 -d $distance
16 <param name="minregions" type="integer" value="2"> 16 -m $minregions
17 <label>min number of intervals per cluster</label> 17 -o $returntype
18 </param> 18 ]]></command>
19 <param name="returntype" type="select" label="Return type"> 19 <inputs>
20 <option value="1">Merge clusters into single intervals</option> 20 <param name="input1" type="data" format="interval" label="Cluster intervals of" />
21 <option value="2">Find cluster intervals; preserve comments and order</option> 21 <param name="distance" type="integer" value="1" label="Max distance between intervals" help="(bp)" />
22 <option value="3">Find cluster intervals; output grouped by clusters</option> 22 <param name="minregions" type="integer" value="2" label="Min number of intervals per cluster" />
23 <option value="4">Find the smallest interval in each cluster</option> 23 <param name="returntype" type="select" label="Return type">
24 <option value="5">Find the largest interval in each cluster</option> 24 <option value="1">Merge clusters into single intervals</option>
25 </param> 25 <option value="2">Find cluster intervals; preserve comments and order</option>
26 </inputs> 26 <option value="3">Find cluster intervals; output grouped by clusters</option>
27 <outputs> 27 <option value="4">Find the smallest interval in each cluster</option>
28 <data format="input" name="output" metadata_source="input1" /> 28 <option value="5">Find the largest interval in each cluster</option>
29 </outputs> 29 </param>
30 <code file="operation_filter.py"> 30 </inputs>
31 <hook exec_after_process="exec_after_cluster" /> 31 <outputs>
32 </code> 32 <data name="output" format_source="input1" metadata_source="input1" />
33 <tests> 33 </outputs>
34 <test> 34 <tests>
35 <param name="input1" value="5.bed" /> 35 <test>
36 <param name="distance" value="1" /> 36 <param name="input1" value="5.bed" />
37 <param name="minregions" value="2" /> 37 <param name="distance" value="1" />
38 <param name="returntype" value="1" /> 38 <param name="minregions" value="2" />
39 <output name="output" file="gops-cluster-1.bed" /> 39 <param name="returntype" value="1" />
40 </test> 40 <output name="output" file="gops-cluster-1.bed" />
41 <test> 41 </test>
42 <param name="input1" value="gops_cluster_bigint.bed" /> 42 <test>
43 <param name="distance" value="1" /> 43 <param name="input1" value="gops_cluster_bigint.bed" />
44 <param name="minregions" value="2" /> 44 <param name="distance" value="1" />
45 <param name="returntype" value="1" /> 45 <param name="minregions" value="2" />
46 <output name="output" file="gops-cluster-1.bed" /> 46 <param name="returntype" value="1" />
47 </test> 47 <output name="output" file="gops-cluster-1.bed" />
48 <test> 48 </test>
49 <param name="input1" value="5.bed" /> 49 <test>
50 <param name="distance" value="1" /> 50 <param name="input1" value="5.bed" />
51 <param name="minregions" value="2" /> 51 <param name="distance" value="1" />
52 <param name="returntype" value="2" /> 52 <param name="minregions" value="2" />
53 <output name="output" file="gops-cluster-2.bed" /> 53 <param name="returntype" value="2" />
54 </test> 54 <output name="output" file="gops-cluster-2.bed" />
55 <test> 55 </test>
56 <param name="input1" value="5.bed" /> 56 <test>
57 <param name="distance" value="1" /> 57 <param name="input1" value="5.bed" />
58 <param name="minregions" value="2" /> 58 <param name="distance" value="1" />
59 <param name="returntype" value="3" /> 59 <param name="minregions" value="2" />
60 <output name="output" file="gops-cluster-3.bed" /> 60 <param name="returntype" value="3" />
61 </test> 61 <output name="output" file="gops-cluster-3.bed" />
62 </tests> 62 </test>
63 <help> 63 </tests>
64 64 <help><![CDATA[
65 .. class:: infomark 65 .. class:: infomark
66 66
67 **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. 67 **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.
68 68
69 ----- 69 @SCREENCASTS@
70
71 **Screencasts!**
72
73 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
74
75 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
76
77 -----
78 70
79 **Syntax** 71 **Syntax**
80 72
81 - **Maximum distance** is greatest distance in base pairs allowed between intervals that will be considered &quot;clustered&quot;. **Negative** values for distance are allowed, and are useful for clustering intervals that overlap. 73 - **Maximum distance** is greatest distance in base pairs allowed between intervals that will be considered &quot;clustered&quot;. **Negative** values for distance are allowed, and are useful for clustering intervals that overlap.
82 - **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. 74 - **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.
93 .. image:: gops_clusterFind.gif 85 .. image:: gops_clusterFind.gif
94 86
95 Merge Clusters: 87 Merge Clusters:
96 88
97 .. image:: gops_clusterMerge.gif 89 .. image:: gops_clusterMerge.gif
98 90 ]]></help>
99 </help>
100 </tool> 91 </tool>