Mercurial > repos > devteam > windowsplitter

annotate windowSplitter.xml @ 3:1011f028f09d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
author devteam
date Wed, 03 Jun 2020 13:44:45 +0000
parents 1fb384fb950e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
1 <tool id="winSplitter" name="Make windows" version="1.0.1">
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
2 <description></description>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
3 <requirements>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
4 <requirement type="package" version="0.8.8">bx-python</requirement>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
5 </requirements>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
6 <command>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
7 python $__tool_directory__/windowSplitter.py
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
8 $input
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
9 $size
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
10 $out_file1
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
11 ${wintype.choice}
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
12 ${wintype.offset}
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
13 -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
14 </command>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
15 <inputs>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
16 <!--<param label="Genome" name="dbkey" type="genomebuild"/>-->
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
17 <param format="interval" name="input" type="data" label="Select data"/>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
18 <param name="size" type="integer" value="500" label="Window size"/>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
19 <conditional name="wintype">
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
20 <param name="choice" type="select" label="Make sliding windows?">
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
21 <option value="0" selected="true">No</option>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
22 <option value="1">Yes</option>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
23 </param>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
24 <when value="0">
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
25 <param name="offset" type="hidden" value="0" />
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
26 </when>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
27 <when value="1">
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
28 <param name="offset" type="integer" value="10" label="Offset size"/>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
29 </when>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
30 </conditional>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
31 </inputs>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
32 <outputs>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
33 <data format="interval" name="out_file1" metadata_source="input"/>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
34 </outputs>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
35 <tests>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
36 <test>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
37 <param name="input" value="4.bed"/>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
38 <param name="size" value="5000"/>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
39 <param name="choice" value="1"/>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
40 <param name="offset" value="4000"/>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
41 <output name="out_file1" file="4_windows.bed"/>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
42 </test>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
43 </tests>
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
44 <help>
0
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
45
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
46 .. class:: infomark
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
47
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
48 **What it does**
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
49
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
50 This tool splits the intervals in the input file into smaller intervals based on the specified window-size and window type.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
51
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
52 -----
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
53
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
54 .. class:: warningmark
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
55
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
56 **Note**
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
57
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
58 The positions at the end of the input interval which do not fit into the last window or a new window of required size, will be omitted from the output.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
59
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
60 -----
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
61
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
62 .. class:: infomark
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
63
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
64 **About formats**
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
65
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
66 **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
67
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
68 The first three BED fields (required) are::
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
69
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
70 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
71 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
72 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
73
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
74 The additional BED fields (optional) are::
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
75
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
76 4. name - The name of the BED line.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
77 5. score - A score between 0 and 1000.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
78 6. strand - Defines the strand - either '+' or '-'.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
79 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
80 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
81 9. reserved - This should always be set to zero.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
82 10. blockCount - The number of blocks (exons) in the BED line.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
83 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
84 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
85 13. expCount - The number of experiments.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
86 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
87 15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
88
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
89 -----
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
90
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
91 **Example**
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
92
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
93 - For the following dataset::
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
94
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
95 chr22 1000 4700 NM_174568 0 +
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
96
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
97 - running this tool with **Window size as 1000**, will return::
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
98
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
99 chr22 1000 2000 NM_174568 0 +
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
100 chr22 2000 3000 NM_174568 0 +
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
101 chr22 3000 4000 NM_174568 0 +
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
102
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
103 - running this tool to make **Sliding windows** of **size 1000** and **offset 500**, will return::
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
104
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
105 chr22 1000 2000 NM_174568 0 +
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
106 chr22 1500 2500 NM_174568 0 +
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
107 chr22 2000 3000 NM_174568 0 +
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
108 chr22 2500 3500 NM_174568 0 +
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
109 chr22 3000 4000 NM_174568 0 +
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
110 chr22 3500 4500 NM_174568 0 +
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
111
3
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
devteam
parents: 2
diff changeset
112 </help>
0
4815516900d4 Imported from capsule None
devteam
parents:
diff changeset
113 </tool>