Mercurial > repos > devteam > divide_pg_snp
annotate dividePgSnpAlleles.xml @ 1:f74fdfc17143 default tip
Removed excess version attributes.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Tue, 03 Dec 2013 12:36:12 -0500 |
| parents | de839553d2a2 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="dividePgSnp" version="1.0.0" name="Separate pgSnp alleles" hidden="false"> |
| 2 <description>into columns</description> | |
| 3 <command interpreter="perl"> | |
| 4 #if $refcol.ref == "yes" #dividePgSnpAlleles.pl -ref=$refcol.ref_column $input1 > $out_file1 | |
| 5 #else #dividePgSnpAlleles.pl $input1 > $out_file1 | |
| 6 #end if | |
| 7 </command> | |
| 8 <inputs> | |
|
1
f74fdfc17143
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
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9 <param format="interval" name="input1" type="data" label="pgSnp dataset" /> |
|
f74fdfc17143
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
10 <conditional name="refcol"> |
|
f74fdfc17143
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
11 <param name="ref" type="select" label="Dataset has a column with the reference allele:"> |
| 0 | 12 <option value="yes">yes</option> |
| 13 <option value="no" selected="true">no</option> | |
| 14 </param> | |
| 15 <when value="yes"> | |
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f74fdfc17143
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
16 <param name="ref_column" type="data_column" data_ref="input1" label="Column with reference allele" /> |
| 0 | 17 </when> |
| 18 <when value="no"> <!-- do nothing --> | |
| 19 </when> | |
| 20 </conditional> | |
| 21 </inputs> | |
| 22 <outputs> | |
|
1
f74fdfc17143
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
23 <data format="interval" name="out_file1" /> |
| 0 | 24 </outputs> |
| 25 <tests> | |
| 26 <test> | |
| 27 <param name='input1' value='dividePgSnp_input.pgSnp' ftype='interval' /> | |
| 28 <param name='ref' value='no' /> | |
|
1
f74fdfc17143
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
29 <param name="output" file="dividePgSnp_output.txt" /> |
| 0 | 30 </test> |
| 31 </tests> | |
| 32 | |
| 33 <help> | |
| 34 **Dataset formats** | |
| 35 | |
| 36 The input dataset is of Galaxy datatype interval_ with the columns specified | |
| 37 for pgSnp_. | |
| 38 Any additional columns beyond the pgSnp defined columns will be appended to | |
| 39 the output. | |
| 40 The output dataset is in interval_ format. (`Dataset missing?`_) | |
| 41 | |
| 42 .. _interval: ./static/formatHelp.html#interval | |
| 43 .. _Dataset missing?: ./static/formatHelp.html | |
| 44 .. _pgSnp: ./static/formatHelp.html#pgSnp | |
| 45 | |
| 46 **What it does** | |
| 47 | |
| 48 This separates the alleles from a pgSnp dataset into separate columns, | |
| 49 as well as the frequencies and scores that go with the alleles. It will skip | |
| 50 any positions with more than 2 alleles. If only a single allele is given then "N" | |
| 51 will be used for the second, with a frequency and score of zero. Or, if a | |
| 52 column with reference alleles is provided, | |
| 53 the value in that column will be used in place of the "N" for single alleles. | |
| 54 | |
| 55 ----- | |
| 56 | |
| 57 **Examples** | |
| 58 | |
| 59 - input pgSnp file:: | |
| 60 | |
| 61 chr1 256 257 A/C 2 3,4 10,20 | |
| 62 chr1 56100 56101 A 1 5 30 | |
| 63 chr1 77052 77053 A/G 2 6,7 40,50 | |
| 64 chr1 110904 110905 A 1 8 60 | |
| 65 etc. | |
| 66 | |
| 67 - output:: | |
| 68 | |
| 69 chr1 256 257 A 3 10 C 4 20 | |
| 70 chr1 56100 56101 A 5 30 N 0 0 | |
| 71 chr1 77052 77053 A 6 40 G 7 50 | |
| 72 chr1 110904 110905 A 8 60 N 0 0 | |
| 73 etc. | |
| 74 | |
| 75 </help> | |
| 76 </tool> |