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comparison hapmap2mlmm/HapmapToMLMMFiles.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="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="1.1"> 1 <tool id="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="2.0.0">
2 <description>converts a hapmap file into MLMM input files</description> 2 <description>Converts a hapmap file into MLMM input files</description>
3 <!-- [STRONGLY RECOMMANDED] Exit code rules --> 3 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
4 <requirements>
5 <requirement type="package" version="4.1.3">gawk</requirement>
6 </requirements>
4 <stdio> 7 <stdio>
5 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> 8 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
6 <exit_code range="1:" level="fatal" /> 9 <exit_code range="1:" level="fatal" />
7 </stdio> 10 </stdio>
8 <command interpreter="bash">./HapmapToMLMMFiles.sh $input $snp_info $genot 11 <command interpreter="bash">./HapmapToMLMMFiles.sh $input $snp_info $genot
24 <param name="input" value="hapmap2mlmm-hapmap" /> 27 <param name="input" value="hapmap2mlmm-hapmap" />
25 <output name="snp_info" file="hapmap2mlmm-result_snp.hapmap" /> 28 <output name="snp_info" file="hapmap2mlmm-result_snp.hapmap" />
26 <output name="genot" file="hapmap2mlmm-result_genot" /> 29 <output name="genot" file="hapmap2mlmm-result_genot" />
27 </test> 30 </test>
28 </tests> 31 </tests>
29 <help> 32 <help><![CDATA[
30
31
32
33 33
34 .. class:: infomark 34 .. class:: infomark
35 35
36 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform 36 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
37 37
38 | **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). 38 | **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).
39 39
40 .. class:: infomark 40 .. class:: infomark
41 41
42 **Galaxy integration** South Green. 42 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
43
44 .. class:: infomark
45
46 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
43 47
44 --------------------------------------------------- 48 ---------------------------------------------------
45
46 49
47 ================= 50 =================
48 HapmapToMLMMFiles 51 HapmapToMLMMFiles
49 ================= 52 =================
50 53
52 Description 55 Description
53 ----------- 56 -----------
54 57
55 | HapmapToMLMMFiles converts a hapmap file into input files compatible with the MLMM software. 58 | HapmapToMLMMFiles converts a hapmap file into input files compatible with the MLMM software.
56 59
60 ------------
61 Dependencies
62 ------------
63 GAWK
64 gawk_ 4.1.3, Conda version
57 65
58 ----------------- 66 .. _gawk: https://anaconda.org/bioconda/gawk
59 Workflow position
60 -----------------
61
62 **Upstream tool**
63
64 =============== ====================== ===========
65 Name output file(s) format
66 =============== ====================== ===========
67 VCF to Hapmap Fasta alignment fasta
68 =============== ====================== ===========
69
70
71 **Downstream tool**
72
73 =========== ========================== =======
74 Name input file(s) format
75 =========== ========================== =======
76 MLMM
77 =========== ========================== =======
78
79
80 67
81 ---------- 68 ----------
82 Input file 69 Input file
83 ---------- 70 ----------
84 71
138 Ind_id SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 SNP11 SNP12 SNP13 SNP14 125 Ind_id SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 SNP11 SNP12 SNP13 SNP14
139 Ind1 0 0 0 0 0 0 2 0 2 0 0 0 2 0 126 Ind1 0 0 0 0 0 0 2 0 2 0 0 0 2 0
140 Ind2 0 0 0 0 0 2 2 0 0 0 0 0 0 0 127 Ind2 0 0 0 0 0 2 2 0 0 0 0 0 0 0
141 128
142 129
143 </help> 130 ]]></help>
144 <citations> 131 <citations>
145 <!-- [HELP] As DOI or BibTex entry --> 132 <!-- [HELP] As DOI or BibTex entry -->
146 <citation type="bibtex">@article{Dereeper03062015, 133 <citation type="bibtex">@article{Dereeper03062015,
147 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}, 134 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},
148 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, 135 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},