annotate extract_primers.xml @ 39:e56023008e36 default tip

Changed revision of package_fisher_0_1_4 to be2fc454d121 Changed revision of package_matplotlib_1_2 to a03ee94316b5
author miller-lab
date Mon, 06 Jul 2015 10:32:24 -0400
parents d6b961721037
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
1 <tool id="gd_extract_primers" name="Pick Primers" version="1.0.0">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
2 <description>: Find suitable PCR primers for SNPs</description>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
3
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
4 <command interpreter="python">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
5 extract_primers.py "--input=$input" "--output=$output" "--primers_loc=${GALAXY_DATA_INDEX_DIR}/gd.primers.loc"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
6 #if $override_metadata.choice == "0":
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
7 "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
8 #else
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
9 "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
10 #end if
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
11 </command>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
12
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
13 <inputs>
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
14 <param format="tabular" name="input" type="data" label="SNP dataset"/>
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
15 <conditional name="override_metadata">
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
16 <param name="choice" type="select" format="integer" label="Choose columns" help="Datasets in gd_snp format have the columns in the metadata, all others need the columns chosen." >
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
17 <option value="0" selected="true">No, get columns from metadata</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
18 <option value="1" >Yes, choose columns</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
19 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
20 <when value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
21 <when value="1">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
22 <param name="scaf_col" type="data_column" data_ref="input" numerical="false" label="Column with scaffold"/>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
23 <param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
24 <param name="species" type="select" label="Choose species">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
25 <options from_file="gd.species.txt">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
26 <column name="name" index="1"/>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
27 <column name="value" index="0"/>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
28 </options>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
29 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
30 </when>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
31 </conditional>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
32 </inputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
33
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
34 <outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
35 <data format="txt" name="output"/>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
36 </outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
37
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
38 <tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
39 <test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
40 <param name="input" value="test_out/select_snps/select_snps.gd_snp" ftype="gd_snp" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
41 <param name="choice" value="0"/>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
42 <output name="output" file="test_out/extract_primers/extract_primers.txt" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
43 </test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
44 </tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
45
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
46
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
47 <help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
48
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
49 **Dataset formats**
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
50
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
51 The input dataset is in tabular_ format and must contain a scaffold or
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
52 chromosome column and a position column. The output dataset is in text_
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
53 format as described below.
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
54 (`Dataset missing?`_)
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
55
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
56 .. _tabular: ./static/formatHelp.html#tab
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
57 .. _text: ./static/formatHelp.html#text
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
58 .. _Dataset missing?: ./static/formatHelp.html
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
59
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
60 -----
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
61
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
62 **What it does**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
63
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
64 This tool extracts primers for SNPs in the dataset using the Primer3 program
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
65 (Steve Rozen and Helen J. Skaletsky, 2000).
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
66 The first line of output for a given SNP reports the name of the assembled
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
67 contig, the SNP's position in the contig, the two variant nucleotides, and
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
68 Primer3's "pair penalty". The next line, if not blank, names restriction
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
69 enzymes (from the user-adjustable list) that differentially cut at that
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
70 site, but do not cut at any other position between and including the
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
71 primer positions. The next lines show the SNP's flanking regions, with
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
72 the SNP position indicated by "n", including the primer positions and an
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
73 additional 3 nucleotides.
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
74 <!-- is this precomputed?? how, where is the user-adjustable list? -->
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
75
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
76 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
77
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
78 **Example**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
79
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
80 - input (gd_snp format)::
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
81
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
82 chr5_30800874_30802049 734 G A chr5 30801606 A 24 0 99 4 11 97 Y 496 0.502 0.033 0.215 6
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
83 chr8_55117827_55119487 994 A G chr8 55118815 G 25 0 102 4 11 96 Y 22 0.502 0.025 2.365 1
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
84 chr9_100484836_100485311 355 C T chr9 100485200 T 27 0 108 6 17 100 Y 190 0.512 0.880 2.733 4
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
85 chr12_3635530_3637738 2101 T C chr12 3637630 T 25 0 102 4 13 93 Y 169 0.554 0.024 0.366 4
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
86 etc.
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
87
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
88 - output::
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
89
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
90 chr5_30800874_30802049 734 G A 0.352964
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
91 BglII,MboI,Sau3AI,Tru9I,XhoII
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
92 1 CTGAAGGTGAGCAGGATTCAGGAGACAGAAAACAAAGCCCAGGCCTGCCCAAGGTGGAAA
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
93 >>>>>>>>>>>>>>>>>>>>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
94
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
95 61 AGTCTAACAACTCGCCCTCTGCTTAnATCTGAGACTCACAGGGATAATAACACACTTGGT
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
96
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
97
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
98 21 CAAGGAATAAACTAGATATTATTCACTCCTCTAGAAGGCTGCCAGGAAAATTGCCTGACT
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
99 &lt;&lt;&lt;&lt;&lt;&lt;&lt;
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
100
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
101 181 TGAACCTTGGCTCTGA
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
102 &lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
103 etc.
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
104
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
105 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
106 </tool>