Mercurial > repos > brasset_jensen > srnapipe

annotate sRNAPipe.xml @ 61:9185ca0a7b43 draft

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Updated package according to recommendations.
author pierre.pouchin
date Wed, 16 Jan 2019 08:18:13 -0500
parents 9645d995fb3c
children e6c4f3e96e47
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1 <tool id="sRNAPipe" name="sRNAPipe" version="1.1">
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2 <description>In-depth study of small RNA</description>
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3 <macros>
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4 <xml name="source">
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5 <conditional name="source">
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6 <param name="source" type="select" label="Will you select the database from your history or use a built-in index?">
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7 <option value="indexed">Use a built-in index</option>
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8 <option value="history">Use one from the history</option>
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9 </param>
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10 <when value="indexed">
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11 <param name="indices" argument="@ARG@" type="select" label="Select a reference genome" help="Also use @BUILD@">
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12 <options from_data_table="bwa_indexes">
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13 <filter type="sort_by" column="2" />
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14 <validator type="no_options" message="No indexes are available" />
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15 </options>
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16 </param>
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17 </when>
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18 <when value="history">
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19 <param name="file" argument="@ARG@" type="data" format="fasta" label="Select a reference from history" />
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20 </when>
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21 </conditional>
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22 </xml>
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23 </macros>
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24 <requirements>
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25 <requirement type="package" version="0.7.12">bwa</requirement>
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26 <requirement type="package" version="2.24">bedtools</requirement>
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27 <requirement type="package" version="1.5">samtools</requirement>
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28 <requirement type="package" version="3.3.2">r-base</requirement>
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29 <requirement type="package" version="5.22.0">perl</requirement>
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30 <requirement type="package" version="2.50">perl-getopt-long</requirement>
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31 <requirement type="package" version="1.17">perl-parallel-forkmanager</requirement>
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32 <requirement type="package" version="0.34" >perl-statistics-r</requirement>
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33 <requirement type="package" version="0.30">perl-string-random</requirement>
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34 <requirement type="package" version="0.38" >perl-file-copy-recursive</requirement>
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35 <requirement type="package" version="0.1" >perl-math-cdf</requirement>
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36 <requirement type="package" version="3.6">r-plotrix</requirement>
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37 <requirement type="package" version="1.14.0">bioconductor-sushi</requirement>
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38 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
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39 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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40 </requirements>
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41 <version_command>perl '$__tool_directory__/bin/sRNAPipe.pl'</version_command>
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42 <command detect_errors="aggressive"><![CDATA[
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43 perl '$__tool_directory__/bin/sRNAPipe.pl'
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44
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45 --fastq '${first_input}'
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46 --fastq_n '${first_input.name}'
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47 #for $input_file in $input_files:
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48 --fastq '${input_file.additional_input}'
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49 --fastq_n '${input_file.additional_input.name}'
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50 #end for
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51
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52 #if $genome.source.source == "history":
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53 --ref '${genome.source.file}'
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54 --build_index
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55 #else:
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56 --ref '${genome.source.indices.fields.path}'
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57 #end if
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58
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59 #if $tRNAs.source.source == "history":
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60 --tRNAs '${tRNAs.source.file}'
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61 --build_tRNAs
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62 #elif $tRNAs.source.source == "none":
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63 --tRNAs "None"
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64 #else:
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65 --tRNAs '${tRNAs.source.indices.fields.path}'
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66 #end if
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67
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68 #if $snRNAs.source.source == "history":
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69 --snRNAs '${snRNAs.source.file}'
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70 --build_snRNAs
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71 #elif $snRNAs.source.source == "none":
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72 --snRNAs "None"
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73 #else:
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74 --snRNAs '${snRNAs.source.indices.fields.path}'
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75 #end if
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76
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77 #if $rRNAs.source.source == "history":
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78 --rRNAs '${rRNAs.source.file}'
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79 --build_rRNAs
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80 #elif $rRNAs.source.source == "none":
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81 --rRNAs "None"
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82 #else:
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83 --rRNAs '${rRNAs.source.indices.fields.path}'
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84 #end if
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85
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86 #if $miRNAs.source.source == "history":
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87 --miRNAs '${miRNAs.source.file}'
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88 --build_miRNAs
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89 #else:
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90 --miRNAs '${miRNAs.source.indices.fields.path}'
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91 #end if
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92
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93 #if $transcripts.source.source == "history":
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94 --transcripts '${transcripts.source.file}'
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95 --build_transcripts
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96 #else:
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97 --transcripts '${transcripts.source.indices.fields.path}'
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98 #end if
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99
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100 #if $TE.source.source == "history":
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101 --TE '${TE.source.file}'
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102 --build_TE
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103 #else:
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104 --TE '${TE.source.indices.fields.path}'
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105 #end if
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106
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107 --si_min $si_min
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108 --si_max $si_max
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109 --pi_min $pi_min
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110 --pi_max $pi_max
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111 --min $min
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112 --max $max
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113
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114 --mis $mis
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115 --misTE $misTE
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116 --dir $html_out.files_path
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117 --html $html_out
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118 --PPPon $PPPon
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119 ]]>
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120 </command>
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121
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122 <inputs>
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123 <param name="first_input" argument="--fastq" type="data" format="fastqsanger" label="fastqsanger (Q33)" help="Also set a name with --fastq_n"/>
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124 <repeat name="input_files" title="Additional Fastq Files">
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125 <param name="additional_input" argument="--fastq" type="data" format="fastqsanger" label="fastqsanger (Q33)" help="Also set a name after each fastq with --fastq_n"/>
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126 </repeat>
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127 <section name="genome" title="Reference genome" expanded="true">
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128 <expand macro="source" arg="--ref" build="--build_index"/>
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129 </section>
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130 <section name="transcripts" title="Transcripts" expanded="true">
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131 <expand macro="source" arg="--transcripts" build="--build_transcripts"/>
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132 </section>
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133 <section name="TE" title="Transposable Elements" expanded="true">
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134 <expand macro="source" arg="--TE" build="--build_TE"/>
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135 </section>
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136 <section name="miRNAs" title="miRNAs" expanded="true">
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137 <expand macro="source" arg="--miRNAs" build="--build_miRNAs"/>
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138 </section>
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139 <section name="snRNAs" title="snRNAs" expanded="true">
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140 <expand macro="source" arg="--snRNAs" build="--build_snRNAs"/>
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141 </section>
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142 <section name="rRNAs" title="rRNAs" expanded="true">
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143 <expand macro="source" arg="--rRNAs" build="--build_rRNAs"/>
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144 </section>
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145 <section name="tRNAs" title="tRNAs" expanded="true">
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146 <expand macro="source" arg="--tRNAs" build="--build_tRNAs"/>
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147 </section>
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148
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149 <param name="min" argument="--min" type="integer" value="18" label="minimum read size"/>
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150 <param name="max" argument="--max" type="integer" value="29" label="maximum read size"/>
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151 <param name="si_min" argument="--si_min" type="integer" value="21" label="lower bound of siRNA range"/>
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152 <param name="si_max" argument="--si_max" type="integer" value="21" label="higher bound of siRNA range"/>
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153 <param name="pi_min" argument="--pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
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154 <param name="pi_max" argument="--pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
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155 <param name="mis" argument="--mis" type="integer" value="0" label="maximal genome mismatches"/>
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156 <param name="misTE" argument="--misTE" type="integer" value="3" label="maximal TE mismatches"/>
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157 <param name="PPPon" argument="--PPPon" type="boolean" checked="true" label="PPPartners"/>
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158 </inputs>
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159 <outputs>
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160 <data format="html" name="html_out" label="${tool.name} on ${first_input.name} (${on_string}): HTML report"/>
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161 <collection type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">
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162 <discover_datasets format ="fastqsanger" pattern="__designation_and_ext__" directory="fastq_dir" />
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163 </collection>
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164 </outputs>
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165 <tests>
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166 <test>
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167 <param name="first_input" value="reads-sample-small.fastq" />
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168 <section name="genome">
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169 <conditional name="source">
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170 <param name="source" value="history" />
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171 <param name="file" value ="genome-small.fa" />
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172 </conditional>
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173 </section>
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174 <section name="transcripts">
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175 <conditional name="source">
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176 <param name="source" value="history" />
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177 <param name="file" value ="transcripts-file-small.fa" />
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178 </conditional>
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179 </section>
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180 <section name="TE">
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181 <conditional name="source">
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182 <param name="source" value="history" />
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183 <param name="file" value ="TE-file-small.fa" />
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184 </conditional>
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185 </section>
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186 <section name="miRNAs">
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187 <conditional name="source">
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188 <param name="source" value="history" />
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189 <param name="file" value ="mirbase-21-dme-hairpins-16jul2015.fa" />
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190 </conditional>
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191 </section>
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192 <section name="snRNAs">
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193 <conditional name="source">
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194 <param name="source" value="history" />
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195 <param name="file" value ="dmel-all-sn-snoRNA-r6.03.fasta" />
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196 </conditional>
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197 </section>
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198 <section name="rRNAs">
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199 <conditional name="source">
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200 <param name="source" value="history" />
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201 <param name="file" value ="dmel-all-rRNA-r6.03.fasta" />
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202 </conditional>
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203 </section>
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204 <section name="tRNAs">
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205 <conditional name="source">
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206 <param name="source" value="history" />
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207 <param name="file" value ="dmel-all-tRNA-r6.03.fasta" />
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208 </conditional>
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209 </section>
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210 <param name="min" value="18" />
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211 <param name="max" value="29" />
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212 <param name="si_min" value="21" />
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213 <param name="si_max" value="21" />
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214 <param name="pi_min" value="23" />
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215 <param name="pi_max" value="29" />
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216 <param name="mis" value="0" />
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217 <param name="misTE" value="3" />
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218 <param name="PPPon" value="true" />
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219 <output name='html_out' file="res.html" compare='diff' lines_diff = '10'/>
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220 <output_collection name="output_fastqsanger" type="list">
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221 <element name="reads-sample-small.fastq_all_mappers" file="fastq_dir/reads-sample-small.fastq_all_mappers.fastq" />
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222 <element name="reads-sample-small.fastq-bonafide_reads-genome" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq" />
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223 <element name="reads-sample-small.fastq-bonafide_reads-genome_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome_uni.fastq" />
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224 <element name="reads-sample-small.fastq-bonafide_reads-TEs" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq" />
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225 <element name="reads-sample-small.fastq-bonafide_reads-TEs_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs_uni.fastq" />
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226 <element name="reads-sample-small.fastq-bonafide_reads-transcripts" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq" />
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227 <element name="reads-sample-small.fastq-bonafide_reads-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq" />
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228 <element name="reads-sample-small.fastq-miRNAs-genome" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq" />
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229 <element name="reads-sample-small.fastq-miRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq" />
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230 <element name="reads-sample-small.fastq-miRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-TEs_uni.fastq" />
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231 <element name="reads-sample-small.fastq-miRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts.fastq" />
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232 <element name="reads-sample-small.fastq-miRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts_uni.fastq" />
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233 <element name="reads-sample-small.fastq-piRNAs-genome" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq" />
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234 <element name="reads-sample-small.fastq-piRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq" />
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235 <element name="reads-sample-small.fastq-piRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq" />
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236 <element name="reads-sample-small.fastq-piRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq" />
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237 <element name="reads-sample-small.fastq-piRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq" />
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238 <element name="reads-sample-small.fastq-piRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq" />
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239 <element name="reads-sample-small.fastq-siRNAs-genome" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq" />
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240 <element name="reads-sample-small.fastq-siRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq" />
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241 <element name="reads-sample-small.fastq-siRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq" />
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242 <element name="reads-sample-small.fastq-siRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq" />
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243 <element name="reads-sample-small.fastq-siRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq" />
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244 <element name="reads-sample-small.fastq-siRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq" />
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245 <element name="reads-sample-small.fastq_unique_mappers" file="fastq_dir/reads-sample-small.fastq_unique_mappers.fastq" />
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246 <element name="reads-sample-small.fastq_unmapped" file="fastq_dir/reads-sample-small.fastq_unmapped.fastq" />
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247 </output_collection>
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248 </test>
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249 </tests>
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250 <help>
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251 **User manual**
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252 "https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"
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253 </help>
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254 <citations>
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255 <citation type="doi">10.1038/nature12962</citation>
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256 <citation type="doi">10.1038/nature11233</citation>
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257 <citation type="doi">10.1186/gb4172</citation>
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258 <citation type="doi">10.1038/nature04916</citation>
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259 <citation type="doi">10.1016/j.cell.2007.01.043</citation>
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260 <citation type="doi">10.1016/j.celrep.2015.02.062</citation>
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261 <citation type="doi">10.1093/bioinformatics/btp324</citation>
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262 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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263 <citation type="doi">10.1002/0471250953.bi1112s47</citation>
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264 <citation type="doi">10.1093/bioinformatics/btu379</citation>
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265 <citation type="doi">10.1002/embr.201337898</citation>
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266 <citation type="doi">10.1038/ncomms13739</citation>
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267 <citation type="doi">10.1093/nar/gkt310</citation>
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268 <citation type="doi">10.1186/s13072-015-0041-5</citation>
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269 <citation type="doi">10.1093/bioinformatics/btu647</citation>
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270 </citations>
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271 </tool>