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1 <tool id="sRNAPipe" name="sRNAPipe" version="1.0">
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40
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2 <description>In-depth study of small RNA</description>
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3 <command interpreter="perl">
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4
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5 ./bin/sRNAPipe.pl
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6
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7 --fastq ${first_input}
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8 --fastq_n ${first_input.name}
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9 #for $input_file in $input_files:
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10 --fastq ${input_file.additional_input}
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11 --fastq_n ${input_file.additional_input.name}
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12 #end for
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13
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14 #if $Genome.refGenomeSource == "history":
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15 --ref "${Genome.ownFile}"
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16 --build_index
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17 #else:
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18 --ref "${Genome.indices.fields.path}"
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19 #end if
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20
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21 #if $tRNAs.refGenomeSource == "history":
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22 --tRNAs "${tRNAs.ownFile}"
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23 --build_tRNAs
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24 #elif $tRNAs.refGenomeSource == "none":
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25 --tRNAs "None"
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26 #else:
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27 --tRNAs "${tRNAs.indices.fields.path}"
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28 #end if
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29
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30 #if $snRNAs.refGenomeSource == "history":
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31 --snRNAs "${snRNAs.ownFile}"
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32 --build_snRNAs
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33 #elif $snRNAs.refGenomeSource == "none":
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34 --snRNAs "None"
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35 #else:
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36 --snRNAs "${snRNAs.indices.fields.path}"
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37 #end if
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38
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39 #if $rRNAs.refGenomeSource == "history":
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40 --rRNAs "${rRNAs.ownFile}"
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41 --build_rRNAs
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42 #elif $rRNAs.refGenomeSource == "none":
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43 --rRNAs "None"
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44 #else:
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45 --rRNAs "${rRNAs.indices.fields.path}"
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46 #end if
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47
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48 #if $miRNAs.refGenomeSource == "history":
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49 --miRNAs "${miRNAs.ownFile}"
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50 --build_miRNAs
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51 #else:
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52 --miRNAs "${miRNAs.indices.fields.path}"
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53 #end if
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54
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55 #if $transcripts.refGenomeSource == "history":
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56 --transcripts "${transcripts.ownFile}"
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57 --build_transcripts
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58 #else:
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59 --transcripts "${transcripts.indices.fields.path}"
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60 #end if
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61
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62 #if $TE.refGenomeSource == "history":
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63 --TE "${TE.ownFile}"
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64 --build_TE
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65 #else:
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66 --TE "${TE.indices.fields.path}"
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67 #end if
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68
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69 --si_min $si_min
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70 --si_max $si_max
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71 --pi_min $pi_min
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72 --pi_max $pi_max
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73 --min $min
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74 --max $max
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75
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76 --mis $mis
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77 --misTE $misTE
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78 --dir $html_out.files_path
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79 --html $html_out
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80 --PPPon $PPPon
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81 </command>
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82
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83 <requirements>
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84 <requirement type="package" version="0.7.12">bwa</requirement>
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85 <requirement type="package" version="2.24">bedtools</requirement>
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86 <requirement type="package" version="1.2">samtools</requirement>
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52
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87 <requirement type="package" version="3.3.2">r-base</requirement>
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88 <requirement type="package" version="5.20.3.1">perl</requirement>
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89 <requirement type="package" version="2.50">perl-getopt-long</requirement>
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90 <requirement type="package" version="1.17">perl-parallel-forkmanager</requirement>
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91 <requirement type="package" version="0.34" >perl-statistics-r</requirement>
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92 <requirement type="package" version="0.30">perl-string-random</requirement>
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52
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93 <requirement type="package" version="3.6">r-plotrix</requirement>
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94 <requirement type="package" version="1.14.0">bioconductor-sushi</requirement>
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95 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
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96 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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40
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97 </requirements>
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98
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99 <inputs>
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100 <param format="fastqsanger" name="first_input" type="data" label="fastqsanger (Q33)" help=""/>
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101 <repeat name="input_files" title="Additional Fastq Files">
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102 <param format="fastqsanger" name="additional_input" type="data" label="fastqsanger (Q33)" help=""/>
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103 </repeat>
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104 <conditional name="Genome">
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105 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
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106 <option value="indexed">Use a built-in index</option>
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107 <option value="history">Use one from the history</option>
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108 </param>
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109 <when value="indexed">
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110 <param name="indices" type="select" label="Select a reference genome">
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111 <options from_data_table="bwa_indexes">
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112 <filter type="sort_by" column="2" />
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113 <validator type="no_options" message="No indexes are available" />
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114 </options>
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115 </param>
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116 </when>
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117 <when value="history">
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118 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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119 </when>
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120 </conditional>
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121 <conditional name="transcripts">
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122 <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?">
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123 <option value="indexed">Use a built-in index</option>
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124 <option value="history">Use one from the history</option>
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125 </param>
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126 <when value="indexed">
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127 <param name="indices" type="select" label="Select a transcripts reference">
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128 <options from_data_table="bwa_indexes">
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129 <filter type="sort_by" column="2" />
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130 <validator type="no_options" message="No indexes are available" />
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131 </options>
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132 </param>
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133 </when>
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134 <when value="history">
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135 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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136 </when>
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137 </conditional>
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138 <conditional name="TE">
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139 <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?">
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140 <option value="indexed">Use a built-in index</option>
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141 <option value="history">Use one from the history</option>
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142 </param>
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143 <when value="indexed">
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144 <param name="indices" type="select" label="Select a TE reference">
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145 <options from_data_table="bwa_indexes">
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146 <filter type="sort_by" column="2" />
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147 <validator type="no_options" message="No indexes are available" />
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148 </options>
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149 </param>
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150 </when>
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151 <when value="history">
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152 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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153 </when>
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154 </conditional>
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155 <conditional name="miRNAs">
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156 <param name="refGenomeSource" type="select" label="Will you select miRNA database from your history or use a built-in index?">
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157 <option value="indexed">Use a built-in index</option>
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158 <option value="history">Use one from the history</option>
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159 </param>
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160 <when value="indexed">
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161 <param name="indices" type="select" label="Select a miRNA reference">
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162 <options from_data_table="bwa_indexes">
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163 <filter type="sort_by" column="2" />
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164 <validator type="no_options" message="No indexes are available" />
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165 </options>
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166 </param>
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167 </when>
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168 <when value="history">
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169 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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170 </when>
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171 </conditional>
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172 <conditional name="snRNAs">
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173 <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?">
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174 <option value="indexed">Use a built-in index</option>
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175 <option value="history">Use one from the history</option>
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176 <option value="none">None</option>
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177 </param>
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178 <when value="indexed">
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179 <param name="indices" type="select" label="Select a snRNAs reference">
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180 <options from_data_table="bwa_indexes">
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181 <filter type="sort_by" column="2" />
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182 <validator type="no_options" message="No indexes are available" />
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183 </options>
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184 </param>
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185 </when>
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186 <when value="history">
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187 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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188 </when>
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189 </conditional>
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190 <conditional name="rRNAs">
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191 <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?">
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192 <option value="indexed">Use a built-in index</option>
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193 <option value="history">Use one from the history</option>
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194 <option value="none">None</option>
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195 </param>
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196 <when value="indexed">
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197 <param name="indices" type="select" label="Select a rRNAs reference">
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198 <options from_data_table="bwa_indexes">
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199 <filter type="sort_by" column="2" />
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200 <validator type="no_options" message="No indexes are available" />
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201 </options>
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202 </param>
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203 </when>
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204 <when value="history">
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205 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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206 </when>
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207 </conditional>
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208 <conditional name="tRNAs">
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209 <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?">
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210 <option value="indexed">Use a built-in index</option>
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211 <option value="history">Use one from the history</option>
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212 <option value="none">None</option>
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213 </param>
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214 <when value="indexed">
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215 <param name="indices" type="select" label="Select a tRNA reference">
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216 <options from_data_table="bwa_indexes">
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217 <filter type="sort_by" column="2" />
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218 <validator type="no_options" message="No indexes are available" />
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219 </options>
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220 </param>
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221 </when>
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222 <when value="history">
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223 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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224 </when>
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225 </conditional>
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226
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227 <param name="min" type="integer" value="18" label="minimum read size"/>
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228 <param name="max" type="integer" value="29" label="maximum read size"/>
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229 <param name="si_min" type="integer" value="21" label="lower bound of siRNA range"/>
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230 <param name="si_max" type="integer" value="21" label="higher bound of siRNA range"/>
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231 <param name="pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
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232 <param name="pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
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233
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234 <param name="mis" type="integer" value="0" label="maximal genome mismatches"/>
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235 <param name="misTE" type="integer" value="3" label="maximal TE mismatches"/>
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236 <param name="PPPon" type="boolean" checked="true" label="PPPartners"/>
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237 </inputs>
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238 <outputs>
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239 <data format="html" name="html_out" label="${tool.name}_${first_input.name}_${on_string}"/>
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240
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241 <collection format ="fastqsanger" type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">
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242 <discover_datasets format ="fastqsanger" pattern="(?P<name>.*)" directory="fastq_dir" />
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243 </collection>
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244
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245 </outputs>
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246 <help>
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247 **User manual**
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248 "https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"
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249 </help>
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250 </tool>
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