Mercurial > repos > devteam > cluster
annotate cluster.xml @ 3:1e895b74f29f draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:49:20 -0400 |
| parents | e84cc9cf3ba1 |
| children | 2108e2dc3d32 |
| rev | line source |
|---|---|
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5167eb4b30ca
Corrected version string.
devteam <devteam@galaxyproject.org>
parents:
0
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1 <tool id="gops_cluster_1" name="Cluster" version="1.0.0"> |
| 0 | 2 <description>the intervals of a dataset</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.7.1">bx-python</requirement> | |
| 5 <requirement type="package" version="1.0.0">galaxy-ops</requirement> | |
| 6 </requirements> | |
| 7 <trackster_conf/> | |
| 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> | |
| 9 <inputs> | |
| 10 <param format="interval" name="input1" type="data"> | |
| 11 <label>Cluster intervals of</label> | |
| 12 </param> | |
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3
1e895b74f29f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
13 <param name="distance" type="integer" value="1" help="(bp)"> |
| 0 | 14 <label>max distance between intervals</label> |
| 15 </param> | |
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3
1e895b74f29f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
2
diff
changeset
|
16 <param name="minregions" type="integer" value="2"> |
| 0 | 17 <label>min number of intervals per cluster</label> |
| 18 </param> | |
| 19 <param name="returntype" type="select" label="Return type"> | |
| 20 <option value="1">Merge clusters into single intervals</option> | |
| 21 <option value="2">Find cluster intervals; preserve comments and order</option> | |
| 22 <option value="3">Find cluster intervals; output grouped by clusters</option> | |
| 23 <option value="4">Find the smallest interval in each cluster</option> | |
| 24 <option value="5">Find the largest interval in each cluster</option> | |
| 25 </param> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data format="input" name="output" metadata_source="input1" /> | |
| 29 </outputs> | |
| 30 <code file="operation_filter.py"> | |
| 31 <hook exec_after_process="exec_after_cluster" /> | |
| 32 </code> | |
| 33 <tests> | |
| 34 <test> | |
| 35 <param name="input1" value="5.bed" /> | |
| 36 <param name="distance" value="1" /> | |
| 37 <param name="minregions" value="2" /> | |
| 38 <param name="returntype" value="1" /> | |
| 39 <output name="output" file="gops-cluster-1.bed" /> | |
| 40 </test> | |
| 41 <test> | |
| 42 <param name="input1" value="gops_cluster_bigint.bed" /> | |
| 43 <param name="distance" value="1" /> | |
| 44 <param name="minregions" value="2" /> | |
| 45 <param name="returntype" value="1" /> | |
| 46 <output name="output" file="gops-cluster-1.bed" /> | |
| 47 </test> | |
| 48 <test> | |
| 49 <param name="input1" value="5.bed" /> | |
| 50 <param name="distance" value="1" /> | |
| 51 <param name="minregions" value="2" /> | |
| 52 <param name="returntype" value="2" /> | |
| 53 <output name="output" file="gops-cluster-2.bed" /> | |
| 54 </test> | |
| 55 <test> | |
| 56 <param name="input1" value="5.bed" /> | |
| 57 <param name="distance" value="1" /> | |
| 58 <param name="minregions" value="2" /> | |
| 59 <param name="returntype" value="3" /> | |
| 60 <output name="output" file="gops-cluster-3.bed" /> | |
| 61 </test> | |
| 62 </tests> | |
| 63 <help> | |
| 64 | |
| 65 .. class:: infomark | |
| 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. | |
| 68 | |
| 69 ----- | |
| 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 | |
| 79 **Syntax** | |
| 80 | |
| 81 - **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. | |
| 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. | |
| 83 - **Merge clusters into single intervals** outputs intervals that span the entire cluster. | |
| 84 - **Find cluster intervals; preserve comments and order** filters out non-cluster intervals while maintaining the original ordering and comments in the file. | |
| 85 - **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. | |
| 86 | |
| 87 ----- | |
| 88 | |
| 89 **Examples** | |
| 90 | |
| 91 Find Clusters: | |
| 92 | |
| 2 | 93 .. image:: gops_clusterFind.gif |
| 0 | 94 |
| 95 Merge Clusters: | |
| 96 | |
| 2 | 97 .. image:: gops_clusterMerge.gif |
| 0 | 98 |
| 99 </help> | |
| 100 </tool> |