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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:52:36 -0400
parents ffbd1de29c28
children 718d04143c31
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3:ffbd1de29c28 4:a10f49d9218a
1 <tool id="gops_join_1" name="Join" version="1.0.0"> 1 <tool id="gops_join_1" name="Join" version="1.0.0">
2 <description>the intervals of two datasets side-by-side</description> 2 <description>the intervals of two datasets side-by-side</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 <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 $fill</command> 7 <code file="operation_filter.py"/>
8 <inputs> 8 <command><![CDATA[
9 <param format="interval" name="input1" type="data" help="First dataset"> 9 python '$__tool_directory__/gops_join.py'
10 <label>Join</label> 10 '$input1'
11 </param> 11 '$input2'
12 <param format="interval" name="input2" type="data" help="Second dataset"> 12 '$output'
13 <label>with</label> 13 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
14 </param> 14 -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
15 <param name="min" type="integer" value="1" help="(bp)"> 15 -m $min
16 <label>with min overlap</label> 16 -f $fill
17 </param> 17 ]]></command>
18 <param name="fill" type="select" label="Return"> 18 <inputs>
19 <option value="none">Only records that are joined (INNER JOIN)</option> 19 <param name="input1" type="data" format="interval" label="Join" help="First dataset" />
20 <option value="right">All records of first dataset (fill null with ".")</option> 20 <param name="input2" type="data" format="interval" label="With" help="Second dataset" />
21 <option value="left">All records of second dataset (fill null with ".")</option> 21 <param name="min" type="integer" value="1" label="With min overlap" help="(bp)" />
22 <option value="both">All records of both datasets (fill nulls with ".")</option> 22 <param name="fill" type="select" label="Return">
23 </param> 23 <option value="none">Only records that are joined (INNER JOIN)</option>
24 </inputs> 24 <option value="right">All records of first dataset (fill null with ".")</option>
25 <outputs> 25 <option value="left">All records of second dataset (fill null with ".")</option>
26 <data format="interval" name="output" metadata_source="input1" /> 26 <option value="both">All records of both datasets (fill nulls with ".")</option>
27 </outputs> 27 </param>
28 <code file="operation_filter.py"/> 28 </inputs>
29 <tests> 29 <outputs>
30 <test> 30 <data name="output" format_source="input1" metadata_source="input1" />
31 <param name="input1" value="1.bed" /> 31 </outputs>
32 <param name="input2" value="2.bed" /> 32 <tests>
33 <param name="min" value="1" /> 33 <test>
34 <param name="fill" value="none" /> 34 <param name="input1" value="1.bed" />
35 <output name="output" file="gops-join-none.dat" /> 35 <param name="input2" value="2.bed" />
36 </test> 36 <param name="min" value="1" />
37 <test> 37 <param name="fill" value="none" />
38 <param name="input1" value="1.bed" /> 38 <output name="output" file="gops-join-none.dat" />
39 <param name="input2" value="2.bed" /> 39 </test>
40 <param name="min" value="1" /> 40 <test>
41 <param name="fill" value="right" /> 41 <param name="input1" value="1.bed" />
42 <output name="output" file="gops-join-right.dat" /> 42 <param name="input2" value="2.bed" />
43 </test> 43 <param name="min" value="1" />
44 <test> 44 <param name="fill" value="right" />
45 <param name="input1" value="1.bed" /> 45 <output name="output" file="gops-join-right.dat" />
46 <param name="input2" value="2.bed" /> 46 </test>
47 <param name="min" value="1" /> 47 <test>
48 <param name="fill" value="left" /> 48 <param name="input1" value="1.bed" />
49 <output name="output" file="gops-join-left.dat" /> 49 <param name="input2" value="2.bed" />
50 </test> 50 <param name="min" value="1" />
51 <test> 51 <param name="fill" value="left" />
52 <param name="input1" value="1.bed" /> 52 <output name="output" file="gops-join-left.dat" />
53 <param name="input2" value="2.bed" /> 53 </test>
54 <param name="min" value="1" /> 54 <test>
55 <param name="fill" value="both" /> 55 <param name="input1" value="1.bed" />
56 <output name="output" file="gops-join-both.dat" /> 56 <param name="input2" value="2.bed" />
57 </test> 57 <param name="min" value="1" />
58 <test> 58 <param name="fill" value="both" />
59 <param name="input1" value="1.bed" /> 59 <output name="output" file="gops-join-both.dat" />
60 <param name="input2" value="2.bed" /> 60 </test>
61 <param name="min" value="500" /> 61 <test>
62 <param name="fill" value="none" /> 62 <param name="input1" value="1.bed" />
63 <output name="output" file="gops-join-none-500.dat" /> 63 <param name="input2" value="2.bed" />
64 </test> 64 <param name="min" value="500" />
65 <test> 65 <param name="fill" value="none" />
66 <param name="input1" value="1.bed" /> 66 <output name="output" file="gops-join-none-500.dat" />
67 <param name="input2" value="2.bed" /> 67 </test>
68 <param name="min" value="100" /> 68 <test>
69 <param name="fill" value="both" /> 69 <param name="input1" value="1.bed" />
70 <output name="output" file="gops-join-both-100.dat" /> 70 <param name="input2" value="2.bed" />
71 </test> 71 <param name="min" value="100" />
72 </tests> 72 <param name="fill" value="both" />
73 <help> 73 <output name="output" file="gops-join-both-100.dat" />
74 74 </test>
75 </tests>
76 <help><![CDATA[
75 .. class:: infomark 77 .. class:: infomark
76 78
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. 79 **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.
78 80
79 ----- 81 @SCREENCASTS@
80
81 **Screencasts!**
82
83 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
84
85 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
86
87 -----
88 82
89 **Syntax** 83 **Syntax**
90 84
91 - **Where overlap** specifies the minimum overlap between intervals that allows them to be joined. 85 - **Where overlap** specifies the minimum overlap between intervals that allows them to be joined.
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. 86 - **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.
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. 87 - **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.
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.** 88 - **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.**
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.** 89 - **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.**
96 90
97 ----- 91 -----
98 92
99 **Examples** 93 **Examples**
100 94
113 .. image:: gops_joinRightOuter.gif 107 .. image:: gops_joinRightOuter.gif
114 108
115 All records of both datasets: 109 All records of both datasets:
116 110
117 .. image:: gops_joinFullOuter.gif 111 .. image:: gops_joinFullOuter.gif
118 112 ]]></help>
119
120 </help>
121 </tool> 113 </tool>