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comparison make_gd_file.xml @ 27:8997f2ca8c7a

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Update to Miller Lab devshed revision bae0d3306d3b
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 15 Jul 2013 10:47:35 -0400
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26:91e835060ad2 27:8997f2ca8c7a
1 <tool id="gd_make_gd_file" name="Make File" version="1.0.0">
2 <description>: Build a gd_snp or gd_genotype file</description>
3
4 <command interpreter="python">
5 #import base64
6 #set $preamble_arg = base64.b64encode(str($preamble_names))
7 #set $species_arg = base64.b64encode(str($species))
8 make_gd_file.py '$input' '$scaffold_col' '$pos_col' '$ref_col' '$rPos_col' '$preamble_arg' '$names' '$species_arg' '$dbkey' '$output_type' '$output'
9 </command>
10
11 <inputs>
12 <param name="input" type="data" format="tabular" label="Input dataset" />
13 <param name="scaffold_col" type="data_column" data_ref="input" label="Column with scaffold/contig" />
14 <param name="pos_col" type="data_column" numerical="true" data_ref="input" label="Column with position" />
15 <param name="ref_col" type="data_column" data_ref="input" label="Column with reference species chromosome" />
16 <param name="rPos_col" type="data_column" numerical="true" data_ref="input" label="Column with reference species position" />
17
18 <param name="preamble_names" type="text" area="true" size="5x40" label="Preamble column names">
19 <sanitizer>
20 <valid initial="string.printable"/>
21 </sanitizer>
22 </param>
23 <param name="names" type="data" format="txt" label="Names dataset" />
24
25 <param name="species" type="text" label="Focus species">
26 <sanitizer>
27 <valid initial="string.printable"/>
28 </sanitizer>
29 </param>
30 <param name="dbkey" type="genomebuild" label="Reference species" />
31
32 <param name="output_type" type="select" label="Output format">
33 <option value="gd_snp" selected="true">gd_snp</option>
34 <option value="gd_genotype">gd_genotype</option>
35 </param>
36 </inputs>
37
38 <outputs>
39 <data name="output" format="gd_snp">
40 <change_format>
41 <when input="output_type" value="gd_genotype" format="gd_genotype" />
42 </change_format>
43 </data>
44 </outputs>
45
46 <!--
47 <tests>
48 <test>
49 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
50 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
51 <param name="lo_coverage" value="0" />
52 <param name="hi_coverage" value="1000" />
53 <param name="low_ind_cov" value="3" />
54 <param name="lo_quality" value="30" />
55 <output name="output" file="test_out/modify_snp_table/modify.gd_snp" />
56 </test>
57 </tests>
58 -->
59
60 <help>
61 **Dataset formats**
62
63 The input datasets are in tabular_ and text_ formats.
64 The output dataset is in gd_snp_ or gd_genotype_ format. (`Dataset missing?`_)
65
66 .. _tabular: ./static/formatHelp.html#tab
67 .. _text: ./static/formatHelp.html#text
68 .. _gd_snp: ./static/formatHelp.html#gd_snp
69 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
70 .. _Dataset missing?: ./static/formatHelp.html
71
72 -----
73
74 **What it does**
75
76 This tool simplifies the job of creating a Galaxy file with format gd_snp
77 or gd_genotype. Often, the most complex part of preparing one of these
78 files is to specify how individuals are related to columns of the table,
79 a task facilitated by this command. Each gd_snp or gd_genotype file
80 typically has columnns giving:
81
82 1. scaffold/contig name
83 2. zero-based position in the scaffold/contig
84 3. reference species chromosome
85 4. zero-based position in the reference species chromosome
86
87 The user needs to specify the columns containing these data. Columns are
88 numbered starting with 1. The user also specifies brief column names for
89 these columns. When the focus species and the reference species are the
90 same, the scaffold/contig name and reference species chromosome columns
91 will be identical, as will the position in the scaffold/contig and
92 position in the reference species chromosome columns.
93
94 To inform Galaxy about the correpondence between individuals and columns
95 of the table, the user directs the tool to a history item that lists
96 the individuals in order. Each line starts with unique name for the
97 individuals (no embedded space or tab character), followed by an arbitrary
98 (possibly empty) set of words that are helpful for specifying groups
99 of individuals.
100 </help>
101 </tool>