root/galaxy-central/tools/rgenetics/rgPedSub.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="rgPedSub1" name="Subset markers:">
2    <code file="rgPedSub_code.py"/>
3
4    <description>region or rs list</description>
5
6    <command interpreter="python">
7        rgPedSub.py $script_file
8    </command>
9
10    <inputs>
11        <page>
12       <param name="title" type="text" size="80" label="Title for output files"
13        help="Descriptive title for new genotype/map files" value="Genotype_Subset" />
14       <param name="input1" type="data" format="lped"
15                label="Current history lPed format data" optional="false"
16        size="120" help="Choose a Linkage Ped format data from your current history" />
17       <param name='relfilter' label = "Filter out family relatedness" type="select"
18             optional="false" size="132"
19         help="Optionally remove related subjects if pedigree identifies founders and their offspring">
20         <option value="all" selected='true'>No filter on relatedness - all subjects passed through</option>
21         <option value="fo" >Founders only (pedigree mother and father ID = "0")</option>
22         <option value="oo" >Offspring only (one randomly chosen if >1 sibs in family)</option>
23                </param>
24
25        </page><page>
26       <conditional name="m">
27                <param name="mtype" type="select"  label="Markers in a genomic interval,or as an rs list?" refresh_on_change='true'
28                help="Indicate the markers to be saved - as a list or as genomic region coordinates">
29                  <option value="grslist" >Cut and paste a list of marker ids as rs numbers</option>
30                  <option value="gregion" selected='true'>Supply genomic coordinates for a region (as UCSC location)</option>
31                </param>
32                <when value="gregion">
33                 <param name="region" type="text" label="Genomic refseq coordinates - chromosome:start-end"
34                        size="120" help="Region to be saved as chr9:119,506,000-119,518,000"/>
35                  <param name="rslist" type="hidden" value='' />
36                </when>
37                <when value="grslist">
38                  <param name="region" value="" type="hidden"/>
39                    <param name="rslist" type="text" area='true' size='15x20' label="marker id (rs) list"
40                        help="Cut and paste, or type a list of marker ids separated by spaces"  />
41                </when>
42        </conditional>
43        </page>
44   </inputs>
45
46   <outputs>
47       <data format="lped" name="output1" metadata_source="input1"/>
48   </outputs>
49
50<configfiles>
51<configfile name="script_file">
52title~~~~$title
53output1~~~~$output1
54userId~~~~$userId
55outformat~~~~lped
56basename~~~~$input1.metadata.base_name
57inped~~~~$input1.extra_files_path/$input1.metadata.base_name
58outdir~~~~$output1.files_path
59relfilter~~~~$relfilter
60#if $m.mtype=='grslist'
61rslist~~~~$m.rslist
62region~~~~
63#else
64rslist~~~~
65region~~~~$m.region
66#end if
67</configfile>
68</configfiles>
69
70<tests>
71 <test>
72    <param name='input1' value='tinywga' ftype='lped' >
73    <metadata name='base_name' value='tinywga' />
74    <composite_data value='tinywga.ped' />
75    <composite_data value='tinywga.map' />
76    <edit_attributes type='name' value='tinywga' />
77    </param>
78    <param name='title' value='rgPedSubtest1' />
79    <param name="region" value="" />
80    <param name="rslist" value="rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" />
81    <param name="relfilter" value="all" />
82    <param name="mtype" value="grslist" />
83    <output name='output1' file='rgtestouts/rgPedSub/rgPedSubtest1.lped' ftype='lped' linesDiff='7'/>
84 </test>
85</tests>
86
87<help>
88
89.. class:: infomark
90
91**Note**
92
93There are 2 forms to complete before the job is ready to be run
94
95  **Page 1**
96
97     give the job a mnemonic descriptive title and select the output format.
98
99     Choose a file containing genotypes and a pedigree from your current history
100
101     The input file must be in linkage ped format.
102
103     If the data are not yet in your history, import from one of the system libraries or upload from your computer using the get data tool
104
105  **Page 2**
106
107     Define the markers to be used. You can supply a UCSC style location as chr:start_offset-end_offset
108
109     or a list of marker ids - rs numbers. You can flip between marker input style by changing the select box.
110
111     If you supply a list, the markers must all be from the same chromosome or region for sensible results.
112
113Run the job and the subset file will eventually appear in your history ready to be used with other tools.
114
115-----
116
117**Syntax**
118
119- **Library Linkage Ped** is a linkage format pedigree file chosen from the system file Library
120- **History Linkage Ped** is a linkage format pedigree file chosen from your current Galaxy History
121- **Region** is the genomic region cut and paste from a UCSC browser location window
122- **Genome Build** is the version of the genome your markers are from - use hg18 for CAMP illumina data
123
124-----
125
126.. class:: infomark
127
128**Summary**
129
130This tool is a special purpose tool to extract genotypes from genotype data in linkage
131pedigree format (separate map file) over a specified genomic region
132The region to be extracted can be described as UCSC browser location, or as a list of
133markers.
134
135It is possible to retain ALL markers by leaving the rslist and region empty if you just want to remove
136all offspring from a pedigree for example
137
138The extracted data will appear in your current history as a new lped data set
139
140Copyright, Ross Lazarus, March 2008 for the Rgenetics project
141Released under the LGPL. See http://www.gnu.org/licenses/lgpl.html for license terms.
142
143</help>
144</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。