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comparison specify_restriction_enzymes.xml @ 0:2c498d40ecde

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author miller-lab
date Mon, 09 Apr 2012 12:03:06 -0400
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1 <tool id="gd_specify_restriction_enzymes" name="Specify" version="1.0.0">
2 <description>a set of restriction enzymes</description>
3
4 <command interpreter="python">
5 specify_restriction_enzymes.py "--input=$input" "--output=$output" "--primers_loc=${GALAXY_DATA_INDEX_DIR}/gd.primers.loc"
6 #if $override_metadata.choice == "0":
7 "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}"
8 #else
9 "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species"
10 #end if
11 "--enzyme_list=$enzymes"
12 </command>
13
14 <inputs>
15 <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/>
16 <conditional name="override_metadata">
17 <param name="choice" type="select" format="integer" label="choose columns">
18 <option value="0" selected="true">No, get columns from metadata</option>
19 <option value="1" >Yes, choose columns</option>
20 </param>
21 <when value="0" />
22 <when value="1">
23 <param name="scaf_col" type="data_column" data_ref="input" numerical="false" label="Column with scaffold"/>
24 <param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/>
25 <param name="species" type="select" label="Choose species">
26 <options from_file="gd.species.txt">
27 <column name="name" index="1"/>
28 <column name="value" index="0"/>
29 </options>
30 </param>
31 </when>
32 </conditional>
33
34 <param name="enzymes" type="select" display="checkboxes" multiple="true" label="Choose enzymes">
35 <options from_file="gd.restriction_enzymes.txt">
36 <column name="name" index="0"/>
37 <column name="value" index="1"/>
38 </options>
39 </param>
40 </inputs>
41
42 <outputs>
43 <data format="wsf" name="output" metadata_source="input"/>
44 </outputs>
45
46 <tests>
47 <test>
48 <param name="input" value="test_out/select_snps/select_snps.wsf" ftype="wsf" />
49 <param name="choice" value="0" />
50 <param name="enzymes" value="Bsp1286I,HaeII,RsaI" />
51 <output name="output" file="test_out/specify_restriction_enzymes/specify_restriction_enzymes.wsf" />
52 </test>
53 </tests>
54
55 <help>
56 **What it does**
57
58 It selects the SNPs that are differentially cut by at least one of the
59 specified restriction enzymes. The enzymes are required to cut the amplified
60 segment (for the specified PCR primers) only at the SNP.
61
62 -----
63
64 **Example**
65
66 - input file::
67
68 chr2_75111355_75112576 314 A C L F chr2 75111676 C F 15 4 53 2 9 48 Y 96 0.369 0.355 0.396 0
69 chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2
70 chr10_7434473_7435447 524 T C S S chr10 7435005 T S 11 5 90 14 0 69 Y 626 0.066 0.406 0.727 0
71 chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1
72 chr15_64470252_64471048 89 G A Y Y chr15 64470341 G Y 5 6 109 14 0 69 Y 312 0.247 0.998 0.393 0
73 chr18_48070585_48071386 514 C T E K chr18 48071100 T K 7 7 46 14 0 69 Y 2 0.200 0.032 0.163 0
74 chr18_50154905_50155664 304 A G Y C chr18 50155208 A Y 4 2 17 5 1 22 Y 8 0.022 0.996 0.128 0
75 chr18_57379354_57380496 315 C T V V chr18 57379669 G V 11 0 60 9 6 62 Y 726 0.118 0.048 0.014 1
76 chr19_14240610_14242055 232 C T A V chr19 14240840 C A 18 8 56 15 5 42 Y 73 0.003 0.153 0.835 0
77 chr19_39866997_39874915 3117 C T P P chr19 39870110 C P 3 7 65 14 2 32 Y 6 0.321 0.911 0.462 4
78 etc.
79
80 - output file::
81
82 chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2
83 chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1
84 chr18_57379354_57380496 315 C T V V chr18 57379669 G V 11 0 60 9 6 62 Y 726 0.118 0.048 0.014 1
85 chr19_39866997_39874915 3117 C T P P chr19 39870110 C P 3 7 65 14 2 32 Y 6 0.321 0.911 0.462 4
86 etc.
87 </help>
88 </tool>