Mercurial > repos > iuc > gemini

comparison gemini_autosomal_recessive.xml @ 2:93bb0cfacefb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Mon, 12 Jan 2015 15:31:50 -0500
parents 720cbfb4190d
children ba3abde6775b
comparison
equal deleted inserted replaced
1:d3c4d0208bb2 2:93bb0cfacefb
7 </macros> 7 </macros>
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 gemini 10 gemini
11 11
12 #if $rec_or_dom == 'recessive': 12 #if str($rec_or_dom) == 'recessive':
13 ## start autosomal_recessive 13 ## start autosomal_recessive
14 autosomal_recessive 14 autosomal_recessive
15 #else: 15 #else:
16 ## start autosomal_dominant 16 ## start autosomal_dominant
17 autosomal_dominant 17 autosomal_dominant
18 #end if 18 #end if
19 19
20 #if $report.report_selector != 'all': 20 #if str($report.report_selector) != 'all':
21 --columns "${report.columns}" 21 --columns "${report.columns}"
22 #end if 22 #end if
23 23
24 #if $filter.filter_selector == 'yes': 24 #if str($filter.filter_selector) == 'yes':
25 --filter "${filter.filter}" 25 --filter "${filter.filter}"
26 #end if 26 #end if
27 27
28 -d $d 28 -d $d
29 #if int($min_kindreds) > 0: 29 #if int($min_kindreds) > 0:
40 <param name="rec_or_dom" type="select" label="Autosomal ..." help=""> 40 <param name="rec_or_dom" type="select" label="Autosomal ..." help="">
41 <option value="recessive">recessive</option> 41 <option value="recessive">recessive</option>
42 <option value="dominant">dominant</option> 42 <option value="dominant">dominant</option>
43 </param> 43 </param>
44 44
45 <param name="infile" type="data" format="sqlite" label="GEMINI database" /> 45 <expand macro="infile" />
46 <expand macro="column_filter" /> 46 <expand macro="column_filter" />
47 <expand macro="filter" /> 47 <expand macro="filter" />
48 <expand macro="min_sequence_depth" /> 48 <expand macro="min_sequence_depth" />
49 <param name="min_kindreds" size="4" type="integer" value="-1" lebel="The min. number of kindreds that must have a candidate variant in a gene" 49 <param name="min_kindreds" size="4" type="integer" value="-1" label="The min. number of kindreds that must have a candidate variant in a gene"
50 help="-1 means default values (--min-kindreds)" /> 50 help="-1 means default values (--min-kindreds)" />
51 51
52 </inputs> 52 </inputs>
53 <outputs> 53 <outputs>
54 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> 54 <data name="outfile" format="tabular" />
55 </outputs> 55 </outputs>
56 <tests> 56 <tests>
57 <test> 57 <test>
58 </test> 58 </test>
59 </tests> 59 </tests>