annotate SNiPloid.xml @ 0:e94de0ea3351 draft default tip

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author dereeper
date Wed, 11 Sep 2013 09:08:15 -0400
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1 <tool id="SNiPloid" name="SNiPloid">
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2 <description>Comparison of SNP between a Tetraploid and its Parental Genomes</description>
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3 <command interpreter="bash">./SNiPloid.sh
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4 $Poly_Analysis.polyornot <!-- $1 -->
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5 #if $Poly_Analysis.polyornot == "poly":
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6
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7 $Poly_Analysis.depthPolyploid1 $Poly_Analysis.depthPolyploid2 <!-- $4 $5 -->
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8 $Poly_Analysis.VCFpolyploid1 $Poly_Analysis.DOCpolyploid1 <!-- $6 $7 -->
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9 $Poly_Analysis.VCFpolyploid2 $Poly_Analysis.DOCpolyploid2 <!-- $8 $9 -->
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10 #else:
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11 $Poly_Analysis.Reference.ref <!-- $2 -->
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12
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13 #if $Poly_Analysis.Reference.ref == "1":
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14 $Poly_Analysis.Reference.genome2Name
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15 #end if
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16
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17 $Poly_Analysis.Reference.depthPolyploid1 $Poly_Analysis.Reference.depthGenome1 <!-- $6 $7 -->
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18 $Poly_Analysis.Reference.VCFpolyploid1 $Poly_Analysis.Reference.DOCpolyploid1 <!-- $8 $9 -->
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19 $Poly_Analysis.Reference.VCFgenome1 $Poly_Analysis.Reference.DOCgenome1 <!-- $10 $11 -->
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20 #if $Poly_Analysis.Reference.ref == "0":
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21 $Poly_Analysis.Reference.depthGenome2 <!-- $12 -->
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22 $Poly_Analysis.Reference.VCFgenome2 $Poly_Analysis.Reference.DOCgenome2 <!-- $13 $14 -->
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23 #end if
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24 #end if
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25 $SNP_csv $SNP_html $SNP_count $SNP_count_csv $enableLowQuality $log
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26 #if $Poly_Analysis.polyornot == "poly":
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27 $Poly_Analysis.value_filter_p1 $Poly_Analysis.value_filter_p2
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28 #end if
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29 #if $annotation.add_annot == "yes":
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30 $annotation.add_annot $annotation.annotation_file $map
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31 #end if
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32 </command>
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33
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34 <inputs>
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35
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36 <conditional name="Poly_Analysis">
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37
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38 <param type="select" name="polyornot" label="Type of analysis">
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39 <option value="poly" selected="True">POLYPLOID vs POLYPLOID</option>
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40 <option value="notpoly">POLYPLOID vs PARENTAL DIPLOID GENOMES</option>
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41 </param>
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42
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43 <when value="poly">
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44 <param type="text" name="depthPolyploid1" label="Minimum read depth at a position to make a call (Polyploid 1)" value="20"/>
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45 <param type="text" name="depthPolyploid2" label="Minimum read depth at a position to make a call (Polyploid 2)" value="20"/>
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46 <param format="vcf" name="VCFpolyploid1" type="data" label="VCF file (Polyploid 1)"/>
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47 <param format="vcf" name="VCFpolyploid2" type="data" label="VCF file (Polyploid 2)"/>
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48 <param format="coverage" name="DOCpolyploid1" type="data" label="Depth of coverage information (Polyploid 1)"/>
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49 <param format="coverage" name="DOCpolyploid2" type="data" label="Depth of coverage information (Polyploid 2)"/>
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50 <param type="text" name="value_filter_p1" label="Minimum minor allele frequency (in %) (Polyploid 1)" value="10"/>
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51 <param type="text" name="value_filter_p2" label="Minimum minor allele frequency (in %) (Polyploid 2)" value="10"/>
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52 </when>
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53
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54 <when value="notpoly">
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55 <conditional name="Reference">
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56
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57 <param type="select" name="ref" label="Reference" help="INTERN (Genome 2 as reference) or EXTERN">
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58 <option value="1" selected="True">INTERN</option>
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59 <option value="0">EXTERN</option>
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60 </param>
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61
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62 <when value="0">
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63 <param type="text" name="depthPolyploid1" label="Minimum read depth at a position to make a call (Polyploid)" value="20"/>
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64 <param type="text" name="depthGenome1" label="Minimum read depth at a position to make a call (Genome 1)" value="20"/>
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65 <param type="text" name="depthGenome2" label="Minimum read depth at a position to make a call (Genome 2)" value="20"/>
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66 <param format="vcf" name="VCFpolyploid1" type="data" label="VCF file (Polyploid)"/>
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67 <param format="vcf" name="VCFgenome1" type="data" label="VCF file (Genome 1)"/>
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68 <param format="vcf" name="VCFgenome2" type="data" label="VCF file (Genome 2)"/>
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69 <param format="coverage" name="DOCpolyploid1" type="data" label="Depth of coverage information (Polyploid)"/>
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70 <param format="coverage" name="DOCgenome1" type="data" label="Depth of coverage information (Genome 1)"/>
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71 <param format="coverage" name="DOCgenome2" type="data" label="Depth of coverage information (Genome2)"/>
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72 </when>
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73
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74 <when value="1">
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75 <param type="text" name="genome2Name" label="Genome 2 Name (Reference)" value="GenomeName"/>
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76 <param type="text" name="depthPolyploid1" label="Minimum read depth at a position to make a call (Polyploid)" value="20"/>
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77 <param type="text" name="depthGenome1" label="Minimum read depth at a position to make a call (Genome 1)" value="20"/>
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78 <param format="vcf" name="VCFpolyploid1" type="data" label="VCF file (Polyploid)"/>
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79 <param format="vcf" name="VCFgenome1" type="data" label="VCF file (Genome 1)" help="VCF file with [Genome 1] vs. [Genome 2] as Reference. /!\ Lost of heterozygosity for [Genome 2]"/>
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80 <param format="coverage" name="DOCpolyploid1" type="data" label="Depth of coverage information (Polyploid)"/>
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81 <param format="coverage" name="DOCgenome1" type="data" label="Depth of coverage information (Genome 1)"/>
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82 </when>
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83
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84 </conditional>
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85
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86 </when>
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87
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88 </conditional>
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89
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90 <conditional name="annotation">
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91 <param name="add_annot" type="select" label="Add a genome annotation file">
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92 <option value="no" selected="True">No annotation available</option>
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93 <option value="yes">Add a genome annotation</option>
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94 </param>
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95 <when value="yes">
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96 <param format="gff3" name="annotation_file" type="data" label="Enter a genome annotation in GFF3 format"/>
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97 </when>
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98 <when value="no">
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99 </when>
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100 </conditional>
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101
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102 <param name="enableLowQuality" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Enable LowQual SNP ?" help="Default : only PASS SNP are considered" />
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103
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104
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105 </inputs>
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106
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107 <outputs>
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108
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109 <data format="txt" name="SNP_csv" label="SNP output" />
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110 <data format="html" name="SNP_html" label="SNP output (HTML)" />
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111 <data format="html" name="SNP_count" label="Synthesis output (HTML)" />
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112 <data format="txt" name="SNP_count_csv" label="Synthesis output" />
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113 <data format="txt" name="log" label="log" />
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114 <data format="png" name="map" label="map" />
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115 </outputs>
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116
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117 <help>
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118 .. class:: infomark
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119
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120 **Program encapsulated in Galaxy by Southgreen**
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121
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122 .. class:: infomark
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123
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124 **SNiPlay utilities**
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125
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126 -----
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127
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128 ==============
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129 Authors:
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130 ==============
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131
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132 **Marine Peralta, Alexis Dereeper**
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133
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134 -----
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135
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136 ==========
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137 Overview
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138 ==========
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139
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140 SNiPloid compares SNP between a tetraploid and its parental genomes, or between two polyploids.
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141
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142 -----
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143
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144 For further informations, please visite the website of the SNiPloid_ software.
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145
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146
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147 .. _SNiPloid: http://sniplay.cirad.fr/cgi-bin/sniploid.cgi
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148
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149
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150 </help>
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151
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152 </tool>