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comparison check_gwas_inputs/CheckGWASInputs.xml @ 10:c6640c49fd01 draft

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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 09:00:24 -0400
parents 98c37a5d67f4
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9:98c37a5d67f4 10:c6640c49fd01
1 <tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.1"> 1 <tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="2.0.0">
2 <description>checks concordance between input files for GWAS analysis</description> 2 <description>Checks concordance between input files for GWAS analysis</description>
3 3
4 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> 4 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
5 <requirements> 5 <requirements>
6 <requirement type="binary">perl</requirement> 6 <requirement type="binary">perl</requirement>
7 </requirements> 7 </requirements>
30 <!-- [HELP] Multiple tests can be defined with different parameters --> 30 <!-- [HELP] Multiple tests can be defined with different parameters -->
31 <test> 31 <test>
32 <param name="hapmap" value="gwas-hapmap" /> 32 <param name="hapmap" value="gwas-hapmap" />
33 <param name="trait" value="gwas-trait" /> 33 <param name="trait" value="gwas-trait" />
34 <output name="out_hapmap" file="gwas-result.hapmap" /> 34 <output name="out_hapmap" file="gwas-result.hapmap" />
35 <output name="out_trait" file="gwas-result.trait" /> 35 <output name="out_trait" file="gwas-result.trait" compare="sim_size" delta="0"/>
36 <output name="stats" file="gwas-result.stats" /> 36 <output name="stats" file="gwas-result.stats" />
37 </test> 37 </test>
38 </tests> 38 </tests>
39 <help> 39 <help><![CDATA[
40 40
41 <![CDATA[
42
43
44 .. class:: infomark 41 .. class:: infomark
45 42
46 **Authors** South Green 43 **Authors** South Green
47 44
48 | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). 45 | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
49 46
50 .. class:: infomark 47 .. class:: infomark
51 48
52 **Galaxy integration** South Green. 49 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
50
51 .. class:: infomark
52
53 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
53 54
54 --------------------------------------------------- 55 ---------------------------------------------------
55
56 56
57 =============== 57 ===============
58 CheckGWASInputs 58 CheckGWASInputs
59 =============== 59 ===============
60 60
62 Description 62 Description
63 ----------- 63 -----------
64 64
65 | CheckGWASInputs checks concordance between input files for GWAS analysis. 65 | CheckGWASInputs checks concordance between input files for GWAS analysis.
66 66
67 67 -----------
68 ----------------- 68 Input files
69 Workflow position 69 -----------
70 -----------------
71
72 **Upstream tool**
73
74 =============== ====================== ===========
75 Name output file(s) format
76 =============== ====================== ===========
77 VCF to Hapmap Hapmap file hapmap
78 =============== ====================== ===========
79
80
81
82
83 ----------
84 Input file
85 ----------
86 70
87 Hapmap file 71 Hapmap file
88 Allelic file in Hapmap format 72 Allelic file in Hapmap format
89 73
90 Trait file 74 Trait file
169 Monomorphic: 0 153 Monomorphic: 0
170 Not biallelic: 0 154 Not biallelic: 0
171 Modified markers: 155 Modified markers:
172 Difference in variation: 0 156 Difference in variation: 0
173 157
174 ]]> 158 ]]></help>
175
176
177 </help>
178 <citations> 159 <citations>
179 <!-- [HELP] As DOI or BibTex entry --> 160 <!-- [HELP] As DOI or BibTex entry -->
180 <citation type="bibtex">@article{Dereeper03062015, 161 <citation type="bibtex">@article{Dereeper03062015,
181 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 162 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel},
182 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, 163 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},