root/galaxy-central/tools/rgenetics/rgfakePhe.xml

リビジョン 2, 5.4 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="fakePhe1" name="Null phenotypes">
2  <description>for testing</description>
3   <code file="rgfakePhe_code.py"/>
4   <command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name'
5   "$title1" '$ppheout' '$ppheout.files_path' '$script_file'
6   </command>
7   <inputs>
8    <page>
9    <param name="infile1"
10         type="data" format="pbed,lped"
11         label="Pedigree from Dataset" />
12        <param name="title1" type="text"
13         value="My null phenos" size="60"
14         label="Title for outputs"/>
15        <param name="dbkey" type="hidden" value='hg18' />
16    </page>
17    <page>
18    <repeat name="fakePhe" title="Phenotypes to simulate under the Null">
19        <param name="pName" type="text" label="Phenotype Name">
20        </param>
21      <conditional name="series">
22        <param name="phetype" type="select" label="Phenotype Distribution">
23          <option value="rnorm" selected="true">Random Normal variate</option>
24          <option value="unif">Random Uniform variate</option>
25          <option value="rgamma">Random Gamma variate</option>
26          <option value="weibull">Random Weibull variate</option>
27          <option value="exponential">Random exponential variate</option>
28          <option value="poisson">Random Poisson variate</option>
29          <option value="cat">Random categorical choice</option>
30        </param>
31        <when value="poisson">
32          <param name="lamb" type="integer" value="2" label="Lambda (mean and variance)" />
33        </when>
34        <when value="rnorm">
35          <param name="Mean" type="float" value="0.0" label="Mean" />
36          <param name="SD" type="float" label="SD" value="1.0"/>
37        </when>
38        <when value="exponential">
39          <param name="Mean" type="float" value="1.0" label="Mean" help="lambda for the exponential will be 1.0/Mean" />=
40        </when>
41        <when value="rgamma">
42          <param name="Alpha" type="float" value="10" label="Alpha">
43          </param>
44          <param name="Beta" type="float" label="Beta" value="1.0">
45          </param>
46        </when>
47        <when value="weibull">
48          <param name="Alpha" type="float" value="10" label="Alpha">
49          </param>
50          <param name="Beta" type="float" label="Beta" value="1.0">
51          </param>
52        </when>
53        <when value="unif">
54          <param name="low" type="float" value="0.0" label="Lowest uniform value">
55          </param>
56          <param name="hi" type="float" label="Highest uniform value" value="1.0"
57           help="A uniform value will be generated from the range specified (low to high) - eg 0.0 to 1.0">
58          </param>
59        </when>
60        <when value="cat">
61          <param name="values" type="text" value="A,B,C" label="Comma separated values to choose from"
62         help = "Each of the comma separated values will have an equal probability of being chosen - eg 'A1,A2,B1,B2'">
63          </param>
64        </when>
65      </conditional>
66    </repeat>
67    </page>
68</inputs>
69<outputs>
70       <data format="pphe" name="ppheout"  metadata_source="infile1" />
71</outputs>
72<configfiles>
73<configfile name="script_file">
74#for $n, $f in enumerate($fakePhe)
75#if $f.series.phetype=='rnorm'
76{'pN':'$f.pName','pT':'rnorm','pP':"{'Mean':'$f.series.Mean', 'SD':'$f.series.SD'}"}
77#elif $f.series.phetype=='rgamma'
78{'pN':'$f.pName','pT':'rgamma','pP':"{'Alpha':'$f.series.Alpha', 'Beta':'$f.series.Beta'}"}
79#elif $f.series.phetype=='poisson'
80{'pN':'$f.pName','pT':'poisson','pP':"{'lamb':'$f.series.lamb',}"}
81#elif $f.series.phetype=='exponential'
82{'pN':'$f.pName','pT':'exponential','pP':"{'Mean':'$f.series.Mean',}"}
83#elif $f.series.phetype=='weibull'
84{'pN':'$f.pName','pT':'weibull','pP':"{'Alpha':'$f.series.Alpha', 'Beta':'$f.series.Beta'}"}
85#elif $f.series.phetype=='cat'
86{'pN':'$f.pName','pT':'$f.series.phetype','pP':"{'values':'$f.series.values'}"}
87#elif $f.series.phetype=='unif'
88{'pN':'$f.pName','pT':'$f.series.phetype','pP':"{'low':'$f.series.low','hi':'$f.series.hi'}"}
89#end if
90#end for
91</configfile>
92</configfiles>
93<help>
94.. class:: infomark
95
96This tool allows you to generate an arbitrary (sort of)
97synthetic phenotype file with measurements drawn from normal,
98gamma, weibull, exponential, uniform or categorical distributions. These are for testing under
99the null hypothesis of no association - the values are random but
100from user specified distributions.
101
102Two output files will appear - one for FBAT and the other for Plink since unfortunately,
103they have slightly differing requirements for the header row.
104
105-----
106
107.. class:: warningmark
108
109This tool is very experimental
110
111-----
112
113- **Pedigree** is a library pedigree file - the id's will be used in the synthetic null phenotypes
114- **Title** is a name to give to the output phenotype file
115
116On the next page, you can add an unlimited number of various kinds of phenotypes including choices for
117categorical ones or distributions with specific parameters
118
119Just keep using the "Add new phenotype" button to add new specifications until you're done.
120Use the Execute button to run the program and generate the null phenotype data.
121The new files will be available on the drop down lists for appropriate tools - eg the
122FBAT format one will be available if you run the FBAT modelling tool.
123
124**Attribution**
125Originally designed and written for the Rgenetics
126series of Galaxy tools, and
127copyright Ross Lazarus 2007 (ross period lazarus at gmail period com)
128Licensed under the terms of the LGPL
129as documented http://www.gnu.org/licenses/lgpl.html
130
131</help>
132</tool>
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