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comparison gemini_de_novo.xml @ 0:285f519dab87 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:57:08 -0500
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children 4aabe53ecfe0
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-1:000000000000 0:285f519dab87
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Identifying potential de novo mutations</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">de_novo</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 gemini @BINARY@
13
14 #if $report.report_selector != 'all':
15 --columns "${report.columns}"
16 #end if
17
18 @CMDLN_SQL_FILTER_FILTER_OPTION@
19
20 #if int($min_kindreds) > 0:
21 --min-kindreds $min_kindreds
22 #end if
23
24 #if str($families).strip():
25 --families "$families"
26 #end if
27
28 $lenient
29 $allow_unaffected
30
31
32 -d $d
33
34 #if int($min_gq) > 0:
35 --min-gq $min_gq
36 #end if
37
38 #if int($gt_pl_max) > -1:
39 --gt-pl-max $gt_pl_max
40 #end if
41
42
43 "${ infile }"
44 > "${ outfile }"
45 ]]>
46 </command>
47 <inputs>
48 <expand macro="infile" />
49 <expand macro="column_filter" />
50 <expand macro="filter" />
51 <expand macro="min_kindreds" />
52 <expand macro="family" />
53 <expand macro="lenient" />
54 <expand macro="unaffected" />
55 <expand macro="min_sequence_depth" />
56 <expand macro="min_gq" />
57 <expand macro="gt_pl_max" />
58 </inputs>
59 <outputs>
60 <data name="outfile" format="tabular" />
61 </outputs>
62 <tests>
63 <test>
64 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
65 <param name="columns" value="gene,ref,alt,impact" />
66 <output name="outfile" file="gemini_de_novo_result.tabular" />
67 </test>
68 </tests>
69 <help>
70 **What it does**
71
72 Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI,
73 you can use this tool for identifying de novo (a.k.a spontaneous) mutations that arise in offspring.
74
75 </help>
76 <expand macro="citations"/>
77 </tool>