annotate dividePgSnpAlleles.xml @ 0:de839553d2a2

Uploaded tool tarball.
author devteam
date Wed, 25 Sep 2013 10:26:17 -0400
parents
children f74fdfc17143
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
1 <tool id="dividePgSnp" version="1.0.0" name="Separate pgSnp alleles" hidden="false">
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
2 <description>into columns</description>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
3 <command interpreter="perl">
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
4 #if $refcol.ref == "yes" #dividePgSnpAlleles.pl -ref=$refcol.ref_column $input1 > $out_file1
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
5 #else #dividePgSnpAlleles.pl $input1 > $out_file1
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
6 #end if
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
7 </command>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
8 <inputs>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
9 <param format="interval" version="1.0.0" name="input1" type="data" label="pgSnp dataset" />
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
10 <conditional version="1.0.0" name="refcol">
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
11 <param version="1.0.0" name="ref" type="select" label="Dataset has a column with the reference allele:">
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
12 <option value="yes">yes</option>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
13 <option value="no" selected="true">no</option>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
14 </param>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
15 <when value="yes">
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
16 <param version="1.0.0" name="ref_column" type="data_column" data_ref="input1" label="Column with reference allele" />
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
17 </when>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
18 <when value="no"> <!-- do nothing -->
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
19 </when>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
20 </conditional>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
21 </inputs>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
22 <outputs>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
23 <data format="interval" version="1.0.0" name="out_file1" />
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
24 </outputs>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
25 <tests>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
26 <test>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
27 <param name='input1' value='dividePgSnp_input.pgSnp' ftype='interval' />
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
28 <param name='ref' value='no' />
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
29 <output version="1.0.0" name="output" file="dividePgSnp_output.txt" />
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
30 </test>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
31 </tests>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
32
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
33 <help>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
34 **Dataset formats**
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
35
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
36 The input dataset is of Galaxy datatype interval_ with the columns specified
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
37 for pgSnp_.
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
38 Any additional columns beyond the pgSnp defined columns will be appended to
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
39 the output.
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
40 The output dataset is in interval_ format. (`Dataset missing?`_)
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
41
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
42 .. _interval: ./static/formatHelp.html#interval
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
43 .. _Dataset missing?: ./static/formatHelp.html
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
44 .. _pgSnp: ./static/formatHelp.html#pgSnp
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
45
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
46 **What it does**
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
47
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
48 This separates the alleles from a pgSnp dataset into separate columns,
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
49 as well as the frequencies and scores that go with the alleles. It will skip
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
50 any positions with more than 2 alleles. If only a single allele is given then "N"
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
51 will be used for the second, with a frequency and score of zero. Or, if a
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
52 column with reference alleles is provided,
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
53 the value in that column will be used in place of the "N" for single alleles.
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
54
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
55 -----
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
56
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
57 **Examples**
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
58
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
59 - input pgSnp file::
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
60
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
61 chr1 256 257 A/C 2 3,4 10,20
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
62 chr1 56100 56101 A 1 5 30
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
63 chr1 77052 77053 A/G 2 6,7 40,50
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
64 chr1 110904 110905 A 1 8 60
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
65 etc.
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
66
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
67 - output::
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
68
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
69 chr1 256 257 A 3 10 C 4 20
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
70 chr1 56100 56101 A 5 30 N 0 0
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
71 chr1 77052 77053 A 6 40 G 7 50
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
72 chr1 110904 110905 A 8 60 N 0 0
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
73 etc.
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
74
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
75 </help>
de839553d2a2 Uploaded tool tarball.
devteam
parents:
diff changeset
76 </tool>