Mercurial > repos > iuc > gemini_mendel_errors

comparison gemini_mendel_errors.xml @ 0:dd963f00f297 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:54:21 -0500
parents
children c5f100ce7da5
comparison
equal deleted inserted replaced
-1:000000000000 0:dd963f00f297
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Identify candidate violations of Mendelian inheritance</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">mendel_errors</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 $only_affected
30
31 -d $d
32
33 #if int($min_gq) > 0:
34 --min-gq $min_gq
35 #end if
36
37 #if int($gt_pl_max) > -1:
38 --gt-pl-max $gt_pl_max
39 #end if
40
41
42 "${ infile }"
43 > "${ outfile }"
44 ]]>
45 </command>
46 <inputs>
47 <expand macro="infile" />
48 <expand macro="column_filter" />
49 <expand macro="filter" />
50 <expand macro="min_kindreds" />
51 <expand macro="family" />
52 <expand macro="lenient" />
53 <!-- this parameter should be allow-unaffected, but unfortunately it is not. -->
54 <param name="only_affected" type="boolean" truevalue="--only-affected" falsevalue="" checked="False" label="Only consider candidates from affected samples." help="(--only-affected)"/>
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_mendel_errors_result.tabular" />
67 </test>
68 </tests>
69 <help>
70 <![CDATA[
71
72 **What it does**
73
74 Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI,
75 you can use this tool for identifying mutations that violate the Mendelian inheritance scheme.
76
77 ]]>
78 </help>
79 <expand macro="citations"/>
80 </tool>