Mercurial > repos > iuc > gemini_amend

comparison gemini_amend.xml @ 0:092ce14766b5 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 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
author iuc
date Tue, 16 Feb 2016 05:54:18 -0500
parents
children 5845a899e87d
comparison
equal deleted inserted replaced
-1:000000000000 0:092ce14766b5
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>