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comparison gemini_mendel_errors.xml @ 0:886fdfe90b01 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
author iuc
date Tue, 16 Feb 2016 05:53:45 -0500
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children 453eb01e00e7
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-1:000000000000 0:886fdfe90b01
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>