Mercurial > repos > iuc > gemini_amend

comparison gemini_amend.xml @ 0:ccd8fdcf82d1 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 08:54:53 -0500
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Amend an already loaded GEMINI database.</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">amend</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 cp "${ infile }" "${ outfile }" &&
13
14 gemini @BINARY@
15 $clear
16 --sample "${ ped }"
17
18 "${ outfile }"
19 ]]>
20 </command>
21 <inputs>
22
23 <expand macro="infile" />
24 <param name="ped" type="data" format="tabular" optional="True" label="Additional sample information file in PED+ format" help="(--sample)" />
25 <param argument="--clear" type="boolean" truevalue="--clear" falsevalue="" checked="False" label="Set all values to None before loading" help="Makes it possible to delete values. Otherwise the old ones are kept"/>
26
27 </inputs>
28 <outputs>
29 <data name="outfile" format="gemini.sqlite" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
34 <param name="ped" value="gemini_amend_input.ped" ftype="tabular" />
35 <output name="outfile" file="gemini_amend_result.db" />
36 </test>
37 </tests>
38 <help>
39 <![CDATA[
40 **What it does**
41
42 Gemini amend adds information about the samples via PED file.
43
44 If you have a sample table in a Gemini db that looks like this::
45
46 sample_id family_id name paternal_id maternal_id sex phenotype hair_color
47 1 1 M10475 0 0 1 1 brown
48 2 1 M10478 M10475 M10500 2 2 blonde
49 3 1 M10500 0 0 2 2 purple
50
51 and you want the change the haircolor of sample 3. And also add some information about the preferred hobbies of some samples.
52
53 You could specify the following PED file. ::
54
55 #family_id name paternal_id maternal_id sex phenotype hair_color hobby
56 1 M10475 None None 1 1 brown fishing
57 1 M10478 M10475 M10500 2 2 red biking
58 1 M10500 None None 2 2 purple
59
60 this results in::
61
62 sample_id family_id name paternal_id maternal_id sex phenotype hair_color hobby
63 1 1 M10475 0 0 1 1 brown fishing
64 2 1 M10478 M10475 M10500 2 2 red biking
65 3 1 M10500 0 0 2 2 purple .
66
67 ]]>
68 </help>
69 <expand macro="citations"/>
70 </tool>