root/galaxy-central/tools/new_operations/join.xml

リビジョン 2, 5.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="gops_join_1" name="Join">
2  <description>the intervals of two queries side-by-side</description>
3  <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>
4  <inputs>
5    <param format="interval" name="input1" type="data" help="First query">
6      <label>Join</label>
7    </param>
8    <param format="interval" name="input2" type="data" help="Second query">
9      <label>with</label>
10    </param>
11    <param name="min" size="4" type="integer" value="1" help="(bp)">
12      <label>with min overlap</label>
13    </param>
14        <param name="fill" type="select" label="Return">
15                <option value="none">Only records that are joined (INNER JOIN)</option>
16                <option value="right">All records of first query (fill null with ".")</option>
17                <option value="left">All records of second query (fill null with ".")</option>
18                <option value="both">All records of both queries (fill nulls with ".")</option>
19        </param>
20   </inputs>
21  <outputs>
22    <data format="interval" name="output" metadata_source="input1" />
23  </outputs>
24  <code file="operation_filter.py"/>
25  <tests>
26    <test>
27      <param name="input1" value="1.bed" />
28      <param name="input2" value="2.bed" />
29      <param name="min" value="1" />
30      <param name="fill" value="none" />
31      <output name="output" file="gops-join-none.dat" />
32    </test>
33    <test>
34      <param name="input1" value="1.bed" />
35      <param name="input2" value="2.bed" />
36      <param name="min" value="1" />
37      <param name="fill" value="right" />
38      <output name="output" file="gops-join-right.dat" />
39    </test>
40    <test>
41      <param name="input1" value="1.bed" />
42      <param name="input2" value="2.bed" />
43      <param name="min" value="1" />
44      <param name="fill" value="left" />
45      <output name="output" file="gops-join-left.dat" />
46    </test>
47    <test>
48      <param name="input1" value="1.bed" />
49      <param name="input2" value="2.bed" />
50      <param name="min" value="1" />
51      <param name="fill" value="both" />
52      <output name="output" file="gops-join-both.dat" />
53    </test>
54    <test>
55      <param name="input1" value="1.bed" />
56      <param name="input2" value="2.bed" />
57      <param name="min" value="500" />
58      <param name="fill" value="none" />
59      <output name="output" file="gops-join-none-500.dat" />
60    </test>
61    <test>
62      <param name="input1" value="1.bed" />
63      <param name="input2" value="2.bed" />
64      <param name="min" value="100" />
65      <param name="fill" value="both" />
66      <output name="output" file="gops-join-both-100.dat" />
67    </test>
68  </tests>
69  <help>
70
71.. class:: infomark
72
73**TIP:** If your query 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.
74
75-----
76
77**Screencasts!**
78
79See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
80
81.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
82
83-----
84
85**Syntax**
86
87- **Where overlap** specifies the minimum overlap between intervals that allows them to be joined.
88- **Return only records that are joined** returns only the records of the first query that join to a record in the second query.  This is analogous to an INNER JOIN.
89- **Return all records of first query (fill null with &quot;.&quot;)** returns all intervals of the first query, and any intervals that do not join an interval from the second query are filled in with a period(.).  This is analogous to a LEFT JOIN.
90- **Return all records of second query (fill null with &quot;.&quot;)** returns all intervals of the second query, and any intervals that do not join an interval from the first query 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.**
91- **Return all records of both queries (fill nulls with &quot;.&quot;)** returns all records from both queries, 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.**
92
93-----
94
95**Example**
96
97If **First query** is::
98
99   chr1 10   100  Query1.1
100   chr1 500  1000 Query1.2
101   chr1 1100 1250 Query1.3
102
103and **Second query** is::
104
105   chr1 20   80   Query2.1
106   chr1 2000 2204 Query2.2
107   chr1 2500 3000 Query2.3
108
109
110The four return options will generate:
111
112
113- **Return only records that are joined**::
114
115   chr1 10 100 Query1.1 chr1 20 80 Query2.1
116
117- **Return all records of first query**::
118
119   chr1 10   100  Query1.1 chr1 20 80 Query2.1
120   chr1 500  1000 Query1.2 .    .  .  .
121   chr1 1100 1250 Query1.3 .    .  .  .
122
123- **Return all records of second query**::
124
125   chr1 10 100 Query1.1 chr1 20   80   Query2.1
126   .    .  .   .        chr1 2000 2204 Query2.2
127   .    .  .   .        chr1 2500 3000 Query2.3
128
129- **Return all records of both queries**::
130
131   chr1 10   100  Query1.1 chr1 20   80   Query2.1
132   chr1 500  1000 Query1.2 .    .    .    .
133   chr1 1100 1250 Query1.3 .    .    .    .
134   .    .    .    .        chr1 2000 2204 Query2.2
135   .    .    .    .        chr1 2500 3000 Query2.3
136   
137
138</help>
139</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。