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1 <tool id="sniplay_plink" name="plink" version="1.0">
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description> - Filter large VCF file</description>
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5
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6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
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7 <requirements>
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8 <requirement type="binary">perl</requirement>
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9 <requirement type="package" version="1.90">plink</requirement>
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10 </requirements>
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11
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12
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13 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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14 <stdio>
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15 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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16 <exit_code range="1:" level="fatal" />
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17 </stdio>
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18
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19 <!-- [REQUIRED] The command to execute -->
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20 <command interpreter="bash">
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21 ./plink.sh $vcf $fileout $filelog $frequency $max_freq $allow_missing $type_p $bound_start $bound_end
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22 #if str( $samples ) == "":
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23 'None'
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24 #else
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25 $samples
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26 #end if
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27 #if str( $chromosomes ) == "":
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28 'None'
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29 #else
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30 $chromosomes
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31 #end if
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32 </command>
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33 <code file="find_indiv.py"/>
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34 <!-- [REQUIRED] Input files and tool parameters -->
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35 <inputs>
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36 <param name="vcf" type="data" format="vcf" optional="false" label="VCF input" />
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37
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38 <param name="samples" type="select" label="Samples" multiple="true" dynamic_options="get_field_samples_options(vcf)" help="Samples to be analyzed." />
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39 <!--<param name="samples" type="text" label="Samples" multiple="true" help="Samples to be analyzed." />-->
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40 <!--<param name="chromosomes" type="select" label="Chromosomes" multiple="true" dynamic_options="get_field_chrs_options(input)" help="Chromosomes to be analyzed." />-->
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41 <param name="frequency" type="float" value="0" label="Minimum MAF" help="Minimum Minor Allele Frequency (MAF)" />
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42 <param name="max_freq" type="float" value="0.5" label="Maximum MAF" help="Maximum Minor Allele Frequency (MAF)" />
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43 <param name="allow_missing" type="float" value="1" min="0" max="1" label="Missing data proportion" help="Allowed missing data proportion per site. Must be comprised between 0 and 1." />
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44 <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." >
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45 <option value="ALL" selected="true">All</option>
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46 <option value="SNP">SNPs only</option>
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47 </param>
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48 <param name="chromosomes" type="text" label="Chromosomes" multiple="true" help="Chromosomes to be analyzed. (Comma-separated list of reference sequences, ex: Chr1,Chr2)" />
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49 <param name="bound_start" type="integer" value="1" label="Lower bound" help="Lower bound for a range of sites to be processed." />
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50 <param name="bound_end" type="integer" value="100000000" label="Upper bound" help="Upper bound for a range of sites to be processed." />
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51 </inputs>
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52
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53 <!-- [REQUIRED] Output files -->
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54 <outputs>
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55 <data name="fileout" format="vcf" label="Plink filtered VCF"/>
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56 <data name="filelog" format="txt" label="Plink logfile" />
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57 </outputs>
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58
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59
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60 <!-- [OPTIONAL] Help displayed in Galaxy -->
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61 <help>
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62
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63 .. class:: infomark
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64
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65 **Authors** Shaun Purcell : plink_
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66
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67 .. _plink: https://www.cog-genomics.org/plink2
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68
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69 | **Please cite** "PLINK: a toolset for whole-genome association and population-based linkage analysis.", Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC, **American Journal of Human Genetics**, 2007
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70
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71 .. class:: infomark
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72
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73 **Galaxy integration** Dereeper Alexis (IRD), Andres Gwendoline (Institut Français de Bioinformatique).
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74
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75 .. class:: infomark
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76
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77 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
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78
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79
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80
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81 </help>
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82
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83 </tool>
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