Mercurial > repos > iuc > gemini_gene_wise
comparison gemini_gene_wise.xml @ 0:99d6e7b1b7f1 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author | iuc |
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date | Thu, 18 Feb 2016 08:55:26 -0500 |
parents | |
children | bc66ebfd4159 |
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-1:000000000000 | 0:99d6e7b1b7f1 |
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> | |
2 <description>Custom genotype filtering by gene</description> | |
3 <macros> | |
4 <import>gemini_macros.xml</import> | |
5 <token name="@BINARY@">gene_wise</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 | |
15 #if int($min_filters) > 0: | |
16 --min_filters $min_filters | |
17 #end if | |
18 | |
19 #if $gt_filter.strip(): | |
20 --gt-filter "${gt_filter}" | |
21 #end if | |
22 | |
23 #if $report.report_selector != 'all': | |
24 --columns "${report.columns}" | |
25 #end if | |
26 | |
27 @CMDLN_SQL_FILTER_FILTER_OPTION@ | |
28 | |
29 "${ infile }" | |
30 > "${ outfile }" | |
31 ]]> | |
32 </command> | |
33 <inputs> | |
34 <expand macro="infile" /> | |
35 | |
36 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filter)"> | |
37 <expand macro="sanitize_query" /> | |
38 </param> | |
39 <param name="min_filters" type="integer" value="0" min="0" label="Minimum number of filters" help="(--min-filters)" /> | |
40 <expand macro="column_filter" /> | |
41 <expand macro="filter" /> | |
42 | |
43 | |
44 </inputs> | |
45 <outputs> | |
46 <data name="outfile" format="tabular" /> | |
47 </outputs> | |
48 <tests> | |
49 <test> | |
50 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" /> | |
51 <param name="gt_filter" value="((gt_depths).(*).(>=1).(all))" /> | |
52 <output name="outfile" file="gemini_gene_wise_result.tabular" /> | |
53 </test> | |
54 </tests> | |
55 <help> | |
56 <![CDATA[ | |
57 **What it does** | |
58 | |
59 The gemini query tool allows querying by variant and the inheritance tools described above enable querying by gene for fixed inheritance patterns. The gene_wise tool allows querying by gene with custom genotype filters to bridge the gap between these tools. | |
60 ]]> | |
61 </help> | |
62 <expand macro="citations"/> | |
63 </tool> |