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1 <tool id="rave" name="RAVE" version="1.0">
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2 <description>- Rapid Allelic Variant Extractor</description>
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3 <!-- Required for the tool to work -->
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4 <!-- Wrapper compatible with Plink v1.90b3k -->
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5 <requirements>
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6 <requirement type="binary">perl</requirement>
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7 <requirement type="package" version="1.90">plink</requirement>
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8 </requirements>
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9 <stdio>
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10 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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11 <exit_code range="1:" level="fatal" />
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12 </stdio>
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13 <command interpreter="perl">./rave.pl
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14 --tool_directory $__tool_directory__
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15 --bfile ${snpdb.fields.path}
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16 #if $filter_var.subpopulation == 'yes':
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17 --keep ${filter_var.population_select.fields.path}
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18 #end if
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19 #if $filter_individuals.individual == 'file':
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20 --keep ${filter_individuals.variety_file}
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21 #else if $filter_individuals.individual == 'list':
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22 --variety_list "${filter_individuals.variety_list}"
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23 #end if
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24 #if $filter_loc.location == 'file':
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25 --extract range ${filter_loc.location_file}
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26 #else if $filter_loc.location == 'list':
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27 --location_list "${filter_loc.location_list}"
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28 #end if
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29 #if $filter_locus.locus == 'file':
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30 --extract range ${filter_locus.locus_file}
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31 #else if $filter_locus.locus == 'list':
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32 --locus_list "${filter_locus.locus_list}"
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33 #end if
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34 --maf $maf
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35 --output_format $output_format
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36 --out $plink_output
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37 </command>
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38 <inputs>
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39 <param name="snpdb" type="select" label="Select SNP DB" help="If your genome of interest is not listed, contact us">
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40 <options from_data_table="plink">
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41 <filter type="sort_by" column="1"/>
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42 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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43 </options>
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44 </param>
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45 <param name="maf" type="float" value="0.01" label="Minor allele frequencies" help="--maf filters out all variants with minor allele frequency below the provided threshold (default 0.01)" />
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46 <conditional name="filter_var">
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47 <param name="subpopulation" type="select" label="Filter SNP based on subpopulation">
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48 <option value="no">No</option>
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49 <option value="yes">Yes</option>
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50 </param>
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51 <when value="no"/>
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52 <when value="yes">
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53 <param name="population_select" type="select" display="radio" label="Subpopulation">
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54 <options from_data_table="subpopulation">
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55 <filter type="sort_by" column="1"/>
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56 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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57 </options>
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58 </param>
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59 </when>
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60 </conditional>
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61 <conditional name="filter_individuals">
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62 <param name="individual" type="select" label="Filter SNP based on individual (This parameter can be empty)">
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63 <option value="file">Upload a file from your history</option>
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64 <option value="list">Cut & Paste your list</option>
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65 </param>
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66 <when value="file">
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67 <param name="variety_file" format="txt" type="data" optional="true" label="Variety list from file" help="One range per line, whitespace-separated (i.e : B001 B001)"/>
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68 </when>
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69 <when value="list">
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70 <param name="variety_list" type="text" area="True" size="5x15" label="Variety list from area" help="One range per line, whitespace-separated (i.e : B001 B001)"/>
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71 </when>
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72 </conditional>
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73
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74 <conditional name="filter_loc">
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75 <param name="location" type="select" label="Filter SNP based on genomic location (This parameter can be empty)">
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76 <option value="file">Upload a file from your history</option>
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77 <option value="list">Cut & Paste your list</option>
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78 </param>
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79 <when value="file">
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80 <param name="location_file" format="txt" type="data" optional="true" label="Range list from file" help="One range per line, whitespace-separated (i.e : 1 100000 120000 chr1)"/>
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81 </when>
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82 <when value="list">
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83 <param name="location_list" type="text" area="True" size="5x15" label="Range list from area" help="One range per line, whitespace-separated (i.e : 1 100000 120000 chr1)"/>
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84 </when>
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85 </conditional>
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86 <conditional name="filter_locus">
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87 <param name="locus" type="select" label="Filter SNP based on specific locus (This parameter can be empty)">
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88 <option value="file">Upload a file from your history</option>
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89 <option value="list">Cut & Paste your list</option>
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90 </param>
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91 <when value="file">
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92 <param name="locus_file" format="txt" type="data" optional="true" label="Locus file (MSU locus name)" help="One locus per line (i.e : LOC_Os01g13620)"/>
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93 </when>
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94 <when value="list">
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95 <param name="locus_list" type="text" area="True" size="5x15" label="Locus list from area (MSU locus name)" help="One range per line (i.e : LOC_Os01g13620)"/>
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96 </when>
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97 </conditional>
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98 <param name="output_format" type="select" label="Select output format" help="--recode creates a new text fileset, after applying sample/variant filters and other operations.">
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99 <option value="vcf">VCF</option>
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100 <option value="bgz">VCF bgzip</option>
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101 <option value="structure">Structure</option>
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102 <option value="beagle">Beagle</option>
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103 <option value="fastphase">fastPHASE</option>
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104 </param>
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105 </inputs>
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106 <outputs>
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107 <data format="vcf" name="plink_output" label="${output_format} output" />
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108 <change_format>
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109 <when input="output_format" value="structure" format="txt" />
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110 <when input="output_format" value="beagle" format="bgzip" />
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111 <when input="output_format" value="fastphase" format="bgzip" />
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112 <when input="output_format" value="bgz" format="bgzip" />
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113 </change_format>
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114 <!--output.recode.strct_in-->
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115 </outputs>
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116 <help>
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117
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118 .. class:: infomark
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119
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120 **Program encapsulated in Galaxy by South Green**
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121
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122 .. class:: infomark
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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 Overview
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128 ==========
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129
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130 **PLINK Overview**
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131
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132 PLINK2
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133 Majority of information in this page is derived from an excellent PLINK_ manual written by Shaun Purcell, Christopher Chang.
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134
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135 .. _PLINK: https://www.cog-genomics.org/plink2
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136
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137 .. class:: infomark
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138
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139 **Galaxy integration** Droc Gaetan (CIRAD), Ruiz Manuel (CIRAD).
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140
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141 .. class:: infomark
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142
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143 **Support** For any questions about Galaxy integration, please send an e-mail to southgreen@cirad.fr
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144
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145
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146 -------
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147
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148 </help>
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149 <citations>
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150 <citation type="doi">10.1186/s13742-015-0047-8</citation>
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151 <citation type="doi">10.1086/519795</citation>
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152 </citations>
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153 </tool>
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154
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