Mercurial > repos > dereeper > sniplay
comparison hapmap2mlmm/HapmapToMLMMFiles.xml @ 10:c6640c49fd01 draft
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author | dereeper |
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date | Mon, 16 Apr 2018 09:00:24 -0400 |
parents | 98c37a5d67f4 |
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9:98c37a5d67f4 | 10:c6640c49fd01 |
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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}, |