Mercurial > repos > iuc > gemini

comparison gemini_de_novo.xml @ 0:720cbfb4190d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Imported from capsule None
author iuc
date Mon, 25 Aug 2014 17:15:54 -0400
parents
children 93bb0cfacefb
comparison
equal deleted inserted replaced
-1:000000000000 0:720cbfb4190d
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Identifying potential de novo mutations</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros>
6 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">de_novo</token>
8 </macros>
9 <command>
10 <![CDATA[
11 gemini @BINARY@
12
13 #if $report.report_selector != 'all':
14 --columns "${report.columns}"
15 #end if
16
17 #if $filter.filter_selector == 'yes':
18 --filter "${filter.filter}"
19 #end if
20 -d $d
21 "${ infile }"
22 > "${ outfile }"
23 ]]>
24 </command>
25 <expand macro="stdio" />
26 <inputs>
27 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
28
29 <expand macro="column_filter" />
30 <expand macro="filter" />
31 <expand macro="min_sequence_depth" />
32 </inputs>
33 <outputs>
34 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
35 </outputs>
36 <tests>
37 <test>
38 </test>
39 </tests>
40 <help>
41 **What it does**
42
43 Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI,
44 you can use this tool for identifying de novo (a.k.a spontaneous) mutations that arise in offspring.
45
46 @CITATION@
47 </help>
48 <expand macro="citations"/>
49 </tool>