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1 <tool id="sRNAPipe" name="sRNAPipe" version="1.0">
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2 <description>In-depth study of small RNA</description>
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3 <command><![CDATA[
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4 perl '$__tool_directory__/bin/sRNAPipe.pl'
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5
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6 --fastq '${first_input}'
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7 --fastq_n '${first_input.name}'
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8 #for $input_file in $input_files:
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9 --fastq '${input_file.additional_input}'
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10 --fastq_n '${input_file.additional_input.name}'
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11 #end for
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12
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13 #if $Genome.refGenomeSource == "history":
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14 --ref '${Genome.ownFile}'
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15 --build_index
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16 #else:
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17 --ref '${Genome.indices.fields.path}'
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18 #end if
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19
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20 #if $tRNAs.refGenomeSource == "history":
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21 --tRNAs '${tRNAs.ownFile}'
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22 --build_tRNAs
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23 #elif $tRNAs.refGenomeSource == "none":
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24 --tRNAs "None"
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25 #else:
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26 --tRNAs '${tRNAs.indices.fields.path}'
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27 #end if
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28
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29 #if $snRNAs.refGenomeSource == "history":
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30 --snRNAs '${snRNAs.ownFile}'
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31 --build_snRNAs
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32 #elif $snRNAs.refGenomeSource == "none":
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33 --snRNAs "None"
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34 #else:
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35 --snRNAs '${snRNAs.indices.fields.path}'
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36 #end if
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37
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38 #if $rRNAs.refGenomeSource == "history":
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39 --rRNAs "${rRNAs.ownFile}"
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40 --build_rRNAs
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41 #elif $rRNAs.refGenomeSource == "none":
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42 --rRNAs "None"
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43 #else:
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44 --rRNAs '${rRNAs.indices.fields.path}'
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45 #end if
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46
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47 #if $miRNAs.refGenomeSource == "history":
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48 --miRNAs '${miRNAs.ownFile}'
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49 --build_miRNAs
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50 #else:
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51 --miRNAs '${miRNAs.indices.fields.path}'
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52 #end if
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53
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54 #if $transcripts.refGenomeSource == "history":
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55 --transcripts '${transcripts.ownFile}'
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56 --build_transcripts
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57 #else:
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58 --transcripts '${transcripts.indices.fields.path}'
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59 #end if
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60
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61 #if $TE.refGenomeSource == "history":
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62 --TE '${TE.ownFile}'
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63 --build_TE
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64 #else:
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65 --TE '${TE.indices.fields.path}'
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66 #end if
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67
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68 --si_min $si_min
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69 --si_max $si_max
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70 --pi_min $pi_min
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71 --pi_max $pi_max
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72 --min $min
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73 --max $max
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74
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75 --mis $mis
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76 --misTE $misTE
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77 --dir $html_out.files_path
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78 --html $html_out
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79 --PPPon $PPPon
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80 ]]>
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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="1.5">samtools</requirement>
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87 <requirement type="package" version="3.3.2">r-base</requirement>
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88 <requirement type="package" version="5.22.0">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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93 <requirement type="package" version="0.38" >perl-file-copy-recursive</requirement>
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94 <requirement type="package" version="0.1" >perl-math-cdf</requirement>
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95 <requirement type="package" version="3.6">r-plotrix</requirement>
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96 <requirement type="package" version="1.14.0">bioconductor-sushi</requirement>
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97 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
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98 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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99 </requirements>
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100
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101 <inputs>
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102 <param format="fastqsanger" name="first_input" type="data" label="fastqsanger (Q33)" help=""/>
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103 <repeat name="input_files" title="Additional Fastq Files">
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104 <param format="fastqsanger" name="additional_input" type="data" label="fastqsanger (Q33)" help=""/>
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105 </repeat>
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106 <conditional name="Genome">
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107 <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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108 <option value="indexed">Use a built-in index</option>
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109 <option value="history">Use one from the history</option>
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110 </param>
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111 <when value="indexed">
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112 <param name="indices" type="select" label="Select a reference genome">
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113 <options from_data_table="bwa_indexes">
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114 <filter type="sort_by" column="2" />
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115 <validator type="no_options" message="No indexes are available" />
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116 </options>
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117 </param>
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118 </when>
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119 <when value="history">
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120 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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121 </when>
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122 </conditional>
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123 <conditional name="transcripts">
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124 <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?">
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125 <option value="indexed">Use a built-in index</option>
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126 <option value="history">Use one from the history</option>
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127 </param>
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128 <when value="indexed">
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129 <param name="indices" type="select" label="Select a transcripts reference">
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130 <options from_data_table="bwa_indexes">
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131 <filter type="sort_by" column="2" />
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132 <validator type="no_options" message="No indexes are available" />
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133 </options>
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134 </param>
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135 </when>
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136 <when value="history">
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137 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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138 </when>
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139 </conditional>
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140 <conditional name="TE">
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141 <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?">
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142 <option value="indexed">Use a built-in index</option>
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143 <option value="history">Use one from the history</option>
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144 </param>
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145 <when value="indexed">
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146 <param name="indices" type="select" label="Select a TE reference">
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147 <options from_data_table="bwa_indexes">
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148 <filter type="sort_by" column="2" />
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149 <validator type="no_options" message="No indexes are available" />
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150 </options>
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151 </param>
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152 </when>
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153 <when value="history">
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154 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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155 </when>
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156 </conditional>
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157 <conditional name="miRNAs">
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158 <param name="refGenomeSource" type="select" label="Will you select miRNA database from your history or use a built-in index?">
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159 <option value="indexed">Use a built-in index</option>
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160 <option value="history">Use one from the history</option>
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161 </param>
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162 <when value="indexed">
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163 <param name="indices" type="select" label="Select a miRNA reference">
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164 <options from_data_table="bwa_indexes">
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165 <filter type="sort_by" column="2" />
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166 <validator type="no_options" message="No indexes are available" />
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167 </options>
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168 </param>
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169 </when>
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170 <when value="history">
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171 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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172 </when>
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173 </conditional>
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174 <conditional name="snRNAs">
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175 <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?">
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176 <option value="indexed">Use a built-in index</option>
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177 <option value="history">Use one from the history</option>
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178 <option value="none">None</option>
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179 </param>
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180 <when value="indexed">
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181 <param name="indices" type="select" label="Select a snRNAs reference">
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182 <options from_data_table="bwa_indexes">
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183 <filter type="sort_by" column="2" />
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184 <validator type="no_options" message="No indexes are available" />
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185 </options>
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186 </param>
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187 </when>
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188 <when value="history">
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189 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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190 </when>
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191 </conditional>
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192 <conditional name="rRNAs">
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193 <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?">
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194 <option value="indexed">Use a built-in index</option>
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195 <option value="history">Use one from the history</option>
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196 <option value="none">None</option>
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197 </param>
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198 <when value="indexed">
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199 <param name="indices" type="select" label="Select a rRNAs reference">
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200 <options from_data_table="bwa_indexes">
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201 <filter type="sort_by" column="2" />
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202 <validator type="no_options" message="No indexes are available" />
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203 </options>
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204 </param>
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205 </when>
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206 <when value="history">
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207 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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208 </when>
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209 </conditional>
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210 <conditional name="tRNAs">
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211 <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?">
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212 <option value="indexed">Use a built-in index</option>
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213 <option value="history">Use one from the history</option>
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214 <option value="none">None</option>
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215 </param>
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216 <when value="indexed">
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217 <param name="indices" type="select" label="Select a tRNA reference">
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218 <options from_data_table="bwa_indexes">
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219 <filter type="sort_by" column="2" />
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220 <validator type="no_options" message="No indexes are available" />
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221 </options>
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222 </param>
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223 </when>
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224 <when value="history">
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225 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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226 </when>
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227 </conditional>
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228
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229 <param name="min" type="integer" value="18" label="minimum read size"/>
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230 <param name="max" type="integer" value="29" label="maximum read size"/>
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231 <param name="si_min" type="integer" value="21" label="lower bound of siRNA range"/>
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232 <param name="si_max" type="integer" value="21" label="higher bound of siRNA range"/>
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233 <param name="pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
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234 <param name="pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
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235
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236 <param name="mis" type="integer" value="0" label="maximal genome mismatches"/>
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237 <param name="misTE" type="integer" value="3" label="maximal TE mismatches"/>
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238 <param name="PPPon" type="boolean" checked="true" label="PPPartners"/>
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239 </inputs>
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240 <outputs>
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241 <data format="html" name="html_out" label="${tool.name}_${first_input.name}_${on_string}"/>
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242
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243 <collection format ="fastqsanger" type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">
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244 <discover_datasets format ="fastqsanger" pattern="(?P<name>.*)" directory="fastq_dir" />
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245 </collection>
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246
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247 </outputs>
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248 <help>
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249 **User manual**
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250 "https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"
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251 </help>
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252 </tool>
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