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comparison pgSnp2gd_snp.xml @ 0:d189d06d23cf draft

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Imported from capsule None
author devteam
date Mon, 28 Jul 2014 11:30:09 -0400
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1 <tool id="pgSnp2gd_snp" name="pgSnp to gd_snp" hidden="false" version="1.0.0">
2 <description>Convert from pgSnp to gd_snp</description>
3 <command interpreter="perl">
4 #if $snptab.tab2 == "yes"
5 #if $snptab.colsOnly == "addColsOnly" #pgSnp2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -addColsOnly -chr=${input1.metadata.chromCol} > $out_file1
6 #else #pgSnp2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -ref=${ref} -chr=${input1.metadata.chromCol} > $out_file1
7 #end if
8 #else #pgSnp2gd_snp.pl $input1 -name=$indName -build=${input1.metadata.dbkey} -ref=${ref} -chr=${input1.metadata.chromCol} > $out_file1
9 #end if
10 </command>
11 <inputs>
12 <param format="tab" name="input1" type="data" label="pgSnp dataset" />
13 <conditional name="snptab">
14 <param name="tab2" type="select" label="Append to gd_snp dataset in history">
15 <option value="yes">yes</option>
16 <option value="no" selected="true">no</option>
17 </param>
18 <when value="yes">
19 <param format="gd_snp" name="input2" type="data" label="gd_snp dataset" />
20 <conditional name="needRef">
21 <param name="colsOnly" type="select" label="Skip new SNPs">
22 <option value="no" selected="true">no</option>
23 <option value="addColsOnly">yes</option>
24 </param>
25 <when value="no">
26 <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" />
27 </when>
28 <when value="addColsOnly"> <!-- do nothing -->
29 </when>
30 </conditional>
31 </when>
32 <when value="no">
33 <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" />
34 </when>
35 </conditional>
36 <param name="indName" type="text" size="20" label="Label for new individual/group" value="na" />
37 </inputs>
38 <outputs>
39 <data format="gd_snp" name="out_file1" />
40 </outputs>
41 <tests>
42 <test>
43 <param name='input1' value='pgSnpTest.ref.txt' ftype='interval' />
44 <param name='tab2' value='no' />
45 <param name='ref' value='8' />
46 <param name='indName' value='na' />
47 <output name="output" file="pgSnp2snp_output.txt" />
48 </test>
49 </tests>
50
51 <help>
52
53 **Dataset formats**
54
55 The input dataset is of Galaxy datatype interval_, with the additional columns
56 required for pgSnp_ format.
57 Any further columns beyond those defined for pgSnp will be ignored.
58 The output dataset is a gd_snp_ table. (`Dataset missing?`_)
59
60 .. _interval: ./static/formatHelp.html#interval
61 .. _pgSnp: ./static/formatHelp.html#pgSnp
62 .. _gd_snp: ./static/formatHelp.html#gd_snp
63 .. _Dataset missing?: ./static/formatHelp.html
64
65 -----
66
67 **What it does**
68
69 This tool converts a pgSnp dataset to gd_snp format, either starting a new
70 dataset or appending to an old one. When appending,
71 if any new SNPs appear only in the pgSnp file they can either be skipped entirely, or
72 backfilled with "-1" (meaning "unknown") for previous individuals/groups in the
73 input gd_snp dataset.
74 If any new SNPs are being added (either by creating a new table or by backfilling),
75 then an extra column with the reference allele must be supplied in the pgSnp dataset,
76 as shown in the example below.
77
78 -----
79
80 **Example**
81
82 - input pgSnp file, with reference allele added::
83
84 chr1 1888681 1888682 C/T 2 4,3 0.8893,0.8453 T
85 chr1 3118325 3118326 T 1 8 0.8796 C
86 chr1 3211457 3211458 A/C 2 17,10 0.8610,0.8576 A
87 etc.
88
89 - gd_snp output::
90
91 chr1 1888681 T C -1 3 4 1 0.8893
92 chr1 3118325 C T -1 0 8 0 0.8796
93 chr1 3211457 A C -1 17 10 1 0.8576
94 etc.
95
96 </help>
97 </tool>