annotate join.xml @ 1:11a49f94d086

Corrected version string.
author devteam <devteam@galaxyproject.org>
date Thu, 10 Apr 2014 13:47:31 -0400
parents e56b47dce68a
children de21bdbb8d28
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
11a49f94d086 Corrected version string.
devteam <devteam@galaxyproject.org>
parents: 0
diff changeset
1 <tool id="gops_join_1" name="Join" version="1.0.0">
0
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
2 <description>the intervals of two datasets side-by-side</description>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
3 <requirements>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
4 <requirement type="package" version="0.7.1">bx-python</requirement>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
5 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
6 </requirements>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
7 <command interpreter="python">gops_join.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} -m $min -f $fill</command>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
8 <inputs>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
9 <param format="interval" name="input1" type="data" help="First dataset">
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
10 <label>Join</label>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
11 </param>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
12 <param format="interval" name="input2" type="data" help="Second dataset">
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
13 <label>with</label>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
14 </param>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
15 <param name="min" size="4" type="integer" value="1" help="(bp)">
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
16 <label>with min overlap</label>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
17 </param>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
18 <param name="fill" type="select" label="Return">
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
19 <option value="none">Only records that are joined (INNER JOIN)</option>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
20 <option value="right">All records of first dataset (fill null with ".")</option>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
21 <option value="left">All records of second dataset (fill null with ".")</option>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
22 <option value="both">All records of both datasets (fill nulls with ".")</option>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
23 </param>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
24 </inputs>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
25 <outputs>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
26 <data format="interval" name="output" metadata_source="input1" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
27 </outputs>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
28 <code file="operation_filter.py"/>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
29 <tests>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
30 <test>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
31 <param name="input1" value="1.bed" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
32 <param name="input2" value="2.bed" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
33 <param name="min" value="1" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
34 <param name="fill" value="none" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
35 <output name="output" file="gops-join-none.dat" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
36 </test>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
37 <test>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
38 <param name="input1" value="1.bed" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
39 <param name="input2" value="2.bed" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
40 <param name="min" value="1" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
41 <param name="fill" value="right" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
42 <output name="output" file="gops-join-right.dat" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
43 </test>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
44 <test>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
45 <param name="input1" value="1.bed" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
46 <param name="input2" value="2.bed" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
47 <param name="min" value="1" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
48 <param name="fill" value="left" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
49 <output name="output" file="gops-join-left.dat" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
50 </test>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
51 <test>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
52 <param name="input1" value="1.bed" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
53 <param name="input2" value="2.bed" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
54 <param name="min" value="1" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
55 <param name="fill" value="both" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
56 <output name="output" file="gops-join-both.dat" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
57 </test>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
58 <test>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
59 <param name="input1" value="1.bed" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
60 <param name="input2" value="2.bed" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
61 <param name="min" value="500" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
62 <param name="fill" value="none" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
63 <output name="output" file="gops-join-none-500.dat" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
64 </test>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
65 <test>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
66 <param name="input1" value="1.bed" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
67 <param name="input2" value="2.bed" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
68 <param name="min" value="100" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
69 <param name="fill" value="both" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
70 <output name="output" file="gops-join-both-100.dat" />
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
71 </test>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
72 </tests>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
73 <help>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
74
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
75 .. class:: infomark
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
76
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
77 **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.
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
78
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
79 -----
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
80
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
81 **Screencasts!**
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
82
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
83 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
84
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
85 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
86
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
87 -----
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
88
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
89 **Syntax**
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
90
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
91 - **Where overlap** specifies the minimum overlap between intervals that allows them to be joined.
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
92 - **Return only records that are joined** returns only the records of the first dataset that join to a record in the second dataset. This is analogous to an INNER JOIN.
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
93 - **Return all records of first dataset (fill null with &quot;.&quot;)** returns all intervals of the first dataset, and any intervals that do not join an interval from the second dataset are filled in with a period(.). This is analogous to a LEFT JOIN.
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
94 - **Return all records of second dataset (fill null with &quot;.&quot;)** returns all intervals of the second dataset, and any intervals that do not join an interval from the first dataset are filled in with a period(.). **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.**
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
95 - **Return all records of both datasets (fill nulls with &quot;.&quot;)** returns all records from both datasets, and fills on either the right or left with periods. **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.**
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
96
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
97 -----
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
98
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
99 **Examples**
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
100
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
101 .. image:: ${static_path}/operation_icons/gops_joinRecordsList.gif
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
102
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
103 Only records that are joined (inner join):
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
104
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
105 .. image:: ${static_path}/operation_icons/gops_joinInner.gif
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
106
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
107 All records of first dataset:
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
108
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
109 .. image:: ${static_path}/operation_icons/gops_joinLeftOuter.gif
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
110
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
111 All records of second dataset:
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
112
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
113 .. image:: ${static_path}/operation_icons/gops_joinRightOuter.gif
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
114
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
115 All records of both datasets:
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
116
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
117 .. image:: ${static_path}/operation_icons/gops_joinFullOuter.gif
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
118
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
119
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
120 </help>
e56b47dce68a Imported from capsule None
devteam
parents:
diff changeset
121 </tool>