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1 <tool id="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="1.1">
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2 <description>converts a hapmap file into MLMM input files</description>
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3 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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4 <stdio>
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5 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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6 <exit_code range="1:" level="fatal" />
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7 </stdio>
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8 <command interpreter="bash">./HapmapToMLMMFiles.sh $input $snp_info $genot
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9 </command>
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10 <inputs>
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11 <param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
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12 </inputs>
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13 <outputs>
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14 <data format="txt" name="snp_info" label="SNP Info file"/>
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15 <data format="txt" name="genot" label="Genotyping file for MLMM"/>
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16 </outputs>
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17
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18 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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19 <tests>
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20 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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21 <!-- [HELP] Multiple tests can be defined with different parameters -->
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22
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23 <test>
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24 <param name="input" value="hapmap2mlmm-hapmap" />
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25 <output name="snp_info" file="hapmap2mlmm-result_snp.hapmap" />
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26 <output name="genot" file="hapmap2mlmm-result_genot" />
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27 </test>
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28 </tests>
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29 <help>
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30
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31
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32
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33
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34 .. class:: infomark
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35
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36 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
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37
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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).
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39
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40 .. class:: infomark
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41
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42 **Galaxy integration** South Green.
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43
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44 ---------------------------------------------------
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45
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46
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47 =================
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48 HapmapToMLMMFiles
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49 =================
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50
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51 -----------
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52 Description
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53 -----------
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54
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55 | HapmapToMLMMFiles converts a hapmap file into input files compatible with the MLMM software.
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56
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57
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58 -----------------
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59 Workflow position
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60 -----------------
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61
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62 **Upstream tool**
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63
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64 =============== ====================== ===========
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65 Name output file(s) format
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66 =============== ====================== ===========
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67 VCF to Hapmap Fasta alignment fasta
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68 =============== ====================== ===========
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69
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70
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71 **Downstream tool**
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72
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73 =========== ========================== =======
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74 Name input file(s) format
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75 =========== ========================== =======
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76 MLMM
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77 =========== ========================== =======
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78
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79
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80
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81 ----------
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82 Input file
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83 ----------
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84
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85 Hapmap file
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86 Allelic file in Hapmap format
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87
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88
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89
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90 ------------
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91 Output files
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92 ------------
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93
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94 SNP Info file
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95
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96 Genotyping file for MLMM
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97
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98
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99
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100 ---------------------------------------------------
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101
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102 ---------------
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103 Working example
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104 ---------------
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105
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106 Input files
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107 ===========
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108
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109 Hapmap file
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110 -----------
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111
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112 ::
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113
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114 rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2
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115 SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA
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116 SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA
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117
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118
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119 Output files
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120 ============
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121
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122 SNP Info file
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123 -------------
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124
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125 ::
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126
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127 SNP Chr Pos
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128 SNP1 1 3102
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129 SNP2 1 4648
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130 SNP3 1 7601
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131
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132
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133 Genotyping file for MLMM
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134 ------------------------
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135
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136 ::
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137
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138 Ind_id SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 SNP11 SNP12 SNP13 SNP14
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139 Ind1 0 0 0 0 0 0 2 0 2 0 0 0 2 0
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140 Ind2 0 0 0 0 0 2 2 0 0 0 0 0 0 0
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141
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142
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143 </help>
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144 <citations>
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145 <!-- [HELP] As DOI or BibTex entry -->
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146 <citation type="bibtex">@article{Dereeper03062015,
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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},
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148 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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149 year = {2015},
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150 doi = {10.1093/nar/gkv351},
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151 abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.},
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152 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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153 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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154 journal = {Nucleic Acids Research}
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155 }
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156
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157 </citation>
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158
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159 </citations>
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160 </tool>
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