Mercurial > repos > brasset_jensen > srnapipe

annotate sRNAPipe.xml @ 73:e19192b12af7 draft

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"planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d0d6dce993374eab03ba61c3fa99963f454ea48c"
author brasset_jensen
date Thu, 26 Aug 2021 11:20:45 +0000
parents b140b740f828
children fe3a93edb210
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73
e19192b12af7 "planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d0d6dce993374eab03ba61c3fa99963f454ea48c"
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1 <tool id="sRNAPipe" name="sRNAPipe" version="1.1.2">
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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" token_arg="Argument" token_build="Build argument" token_ref="">
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5 <conditional name="source">
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6 <param name="source" type="select" label="Will you select the reference 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 @REF@">
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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 @REF@ from history" help="We will also use @BUILD@"/>
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20 </when>
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21 </conditional>
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22 </xml>
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23 <xml name="conditional_source" token_arg="Argument" token_build="Build argument" token_ref="" token_name="">
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24 <conditional name="@NAME@">
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25 <param name="use_ref" type="select" label="Use @REF@?">
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26 <option value="true">Yes</option>
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27 <option value="false" selected="true">No</option>
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28 </param>
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29 <when value="true">
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30 <expand macro="source" arg="@ARG@" build="@BUILD@" ref="@REF@"/>
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31 </when>
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32 <when value="false"/>
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33 </conditional>
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34 </xml>
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35 </macros>
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36 <requirements>
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37 <requirement type="package" version="1.1.1">srnapipe</requirement>
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38 </requirements>
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39 <version_command>srnapipe | grep 'version' | grep "version" | cut -d ' ' -f 3</version_command>
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40 <command detect_errors="aggressive"><![CDATA[
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41 srnapipe
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42 #if str($inputs.custom) == 'true'
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43 #for $x in $inputs.inputs
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44 --fastq '$x.fastq'
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45 --fastq_n '$x.fastq_n'
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46 #end for
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47 #else
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48 #for $x in $inputs.fastq
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49 --fastq '$x'
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50 --fastq_n '$x.element_identifier'
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51 #end for
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52 #end if
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53 --min $min
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54 --max $max
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55
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56 #if $genome.source.source == "history"
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57 --ref '$genome.source.file'
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58 --build_index
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59 #else
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60 --ref '$genome.source.indices.fields.path'
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61 #end if
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62 --mis $genome.mis
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63
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64 #if $transcripts.source.source == "history"
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65 --transcripts '$transcripts.source.file'
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66 --build_transcripts
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67 #else
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68 --transcripts '$transcripts.source.indices.fields.path'
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69 #end if
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70
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71 #if $te.source.source == "history"
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72 --TE '$te.source.file'
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73 --build_TE
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74 #else
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75 --TE '$te.source.indices.fields.path'
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76 #end if
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77 --misTE $te.misTE
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78
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79 #if $mirnas.source.source == "history"
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80 --miRNAs '$mirnas.source.file'
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81 --build_miRNAs
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82 #else:
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83 --miRNAs '$mirnas.source.indices.fields.path'
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84 #end if
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85
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86 #if str($snrnas.snrnas.use_ref) == 'true'
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87 #if str($snrnas.snrnas.source.source) == "history"
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88 --snRNAs '$snrnas.snrnas.source.file'
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89 --build_snRNAs
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90 #else
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91 --snRNAs '$snrnas.snrnas.source.indices.fields.path'
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92 #end if
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93 #else
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94 --snRNAs "None"
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95 #end if
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96
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97 #if str($rrnas.rrnas.use_ref) == 'true'
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98 #if str($rrnas.rrnas.source.source) == "history"
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99 --rRNAs '$rrnas.rrnas.source.file'
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100 --build_rRNAs
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101 #else
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102 --rRNAs '$rrnas.rrnas.source.indices.fields.path'
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103 #end if
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104 #else
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105 --rRNAs "None"
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106 #end if
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107
69
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108 #if str($trnas.trnas.use_ref) == 'true'
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109 #if str($trnas.trnas.source.source) == "history"
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110 --tRNAs '$trnas.trnas.source.file'
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111 --build_tRNAs
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112 #else
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113 --tRNAs '$trnas.trnas.source.indices.fields.path'
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114 #end if
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115 #else
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116 --tRNAs "None"
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117 #end if
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118
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119 --si_min $sirna.si_min
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120 --si_max $sirna.si_max
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121 --pi_min $pirna.pi_min
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122 --pi_max $pirna.pi_max
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123 --dir $html_out.files_path
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124 --html $html_out
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125 --PPPon $PPPon
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126 --threads \${GALAXY_SLOTS:-4}
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127 ]]>
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128 </command>
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129 <inputs>
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130 <conditional name="inputs">
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131 <param name="custom" type="select" label="Use custom name for the input sequence files?">
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132 <option value="true">Yes</option>
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133 <option value="false" selected="true">No: the names will be extracted automatically</option>
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134 </param>
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135 <when value="true">
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136 <repeat name="inputs" title="Input sequences" min="1">
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137 <param argument="--fastq" type="data" format="fastqsanger" label="Input sequences"/>
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138 <param argument="--fastq_n" type="text" value="" label="Label for the input sequences"/>
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139 </repeat>
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140 </when>
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141 <when value="false">
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142 <param argument="--fastq" type="data" format="fastqsanger" multiple="true" label="Input sequences" help="Also set a name with --fastq_n"/>
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143 </when>
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144 </conditional>
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145 <param argument="--min" type="integer" value="18" label="Minimum read size"/>
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146 <param argument="--max" type="integer" value="29" label="Maximum read size"/>
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147 <section name="genome" title="Reference genome" expanded="true">
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148 <expand macro="source" arg="--ref" build="--build_index" ref="a reference genome"/>
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149 <param argument="--mis" type="integer" value="0" label="Maximal genome mismatches"/>
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150 </section>
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151 <section name="transcripts" title="Transcripts" expanded="true">
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152 <expand macro="source" arg="--transcripts" build="--build_transcripts" ref="reference transcript sequences"/>
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153 </section>
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154 <section name="te" title="Transposable Elements" expanded="true">
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155 <expand macro="source" arg="--TE" build="--build_TE" ref="reference TE sequences"/>
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156 <param argument="--misTE" type="integer" value="3" label="maximal TE mismatches"/>
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157 </section>
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158 <section name="mirnas" title="miRNAs" expanded="true">
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159 <expand macro="source" arg="--miRNAs" build="--build_miRNAs" ref="reference miRNAs sequences"/>
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160 </section>
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161 <section name="snrnas" title="snRNAs" expanded="true">
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162 <expand macro="conditional_source" name="snrnas" arg="--snRNAs" build="--build_snRNAs" ref="reference snRNAs sequences"/>
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163 </section>
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164 <section name="rrnas" title="rRNAs" expanded="true">
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165 <expand macro="conditional_source" name="rrnas" arg="--rRNAs" build="--build_rRNAs" ref="reference rRNAs sequences"/>
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166 </section>
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167 <section name="trnas" title="tRNAs" expanded="true">
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168 <expand macro="conditional_source" name="trnas" arg="--tRNAs" build="--build_tRNAs" ref="reference tRNAs sequences"/>
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169 </section>
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170 <section name="sirna" title="siRNA" expanded="true">
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171 <param argument="--si_min" type="integer" value="21" label="Lower bound for siRNA range"/>
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172 <param argument="--si_max" type="integer" value="21" label="Higher bound of siRNA range"/>
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173 </section>
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174 <section name="pirna" title="piRNA" expanded="true">
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175 <param argument="--pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
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176 <param argument="--pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
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177 </section>
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178 <param name="PPPon" argument="--PPPon" type="boolean" truevalue="true" falsevalue="false" checked="true" label="PPPartners"/>
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179 </inputs>
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180 <outputs>
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181 <data format="html" name="html_out" label="${tool.name} on ${on_string}: HTML report"/>
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182 <collection type="list" label="${tool.name} on ${on_string}: FastQ outputs" name="output_fastqsanger">
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183 <discover_datasets format ="fastqsanger" pattern="__designation_and_ext__" directory="fastq_dir" />
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184 </collection>
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185 </outputs>
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186 <tests>
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187 <test>
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188 <conditional name="inputs">
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189 <param name="custom" value="false"/>
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190 <param name="fastq" value="reads-sample-small.fastq"/>
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191 </conditional>
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192 <param name="min" value="18" />
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193 <param name="max" value="29" />
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194 <section name="genome">
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195 <conditional name="source">
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196 <param name="source" value="history" />
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197 <param name="file" value ="genome-small.fa" />
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198 </conditional>
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199 <param name="mis" value="0" />
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200 </section>
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201 <section name="transcripts">
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202 <conditional name="source">
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203 <param name="source" value="history" />
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204 <param name="file" value ="transcripts-file-small.fa" />
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205 </conditional>
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206 </section>
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207 <section name="te">
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208 <conditional name="source">
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209 <param name="source" value="history" />
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210 <param name="file" value ="TE-file-small.fa" />
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211 </conditional>
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212 <param name="misTE" value="3" />
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213 </section>
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214 <section name="mirnas">
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215 <conditional name="source">
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216 <param name="source" value="history" />
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217 <param name="file" value ="mirbase-21-dme-hairpins-16jul2015.fa" />
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218 </conditional>
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219 </section>
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220 <section name="snrnas">
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221 <conditional name="snrnas">
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222 <param name="use_ref" value="true"/>
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223 <conditional name="source">
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224 <param name="source" value="history" />
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225 <param name="file" value ="dmel-all-sn-snoRNA-r6.03.fasta" />
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226 </conditional>
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227 </conditional>
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228 </section>
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229 <section name="rrnas">
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230 <conditional name="rrnas">
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231 <param name="use_ref" value="true"/>
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232 <conditional name="source">
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233 <param name="source" value="history" />
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234 <param name="file" value ="dmel-all-rRNA-r6.03.fasta" />
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235 </conditional>
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236 </conditional>
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237 </section>
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238 <section name="trnas">
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239 <conditional name="trnas">
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240 <param name="use_ref" value="true"/>
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241 <conditional name="source">
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242 <param name="source" value="history" />
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243 <param name="file" value ="dmel-all-tRNA-r6.03.fasta" />
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244 </conditional>
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245 </conditional>
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246 </section>
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247 <section name="sirna">
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248 <param name="si_min" value="21" />
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249 <param name="si_max" value="21" />
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250 </section>
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251 <section name="pirna">
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252 <param name="pi_min" value="23" />
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253 <param name="pi_max" value="29" />
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254 </section>
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255 <param name="PPPon" value="true" />
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256 <output name='html_out' file="res.html" compare='diff' lines_diff = '10'/>
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257 <output_collection name="output_fastqsanger" type="list">
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258 <element name="reads-sample-small.fastq_all_mappers" file="fastq_dir/reads-sample-small.fastq_all_mappers.fastq" />
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259 <element name="reads-sample-small.fastq-bonafide_reads-genome" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq" />
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260 <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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261 <element name="reads-sample-small.fastq-bonafide_reads-TEs" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq" />
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262 <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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263 <element name="reads-sample-small.fastq-bonafide_reads-transcripts" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq" />
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264 <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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265 <element name="reads-sample-small.fastq-miRNAs-genome" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq" />
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266 <element name="reads-sample-small.fastq-miRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq" />
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267 <element name="reads-sample-small.fastq-miRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-TEs_uni.fastq" />
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268 <element name="reads-sample-small.fastq-miRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts.fastq" />
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269 <element name="reads-sample-small.fastq-miRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts_uni.fastq" />
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270 <element name="reads-sample-small.fastq-piRNAs-genome" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq" />
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271 <element name="reads-sample-small.fastq-piRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq" />
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272 <element name="reads-sample-small.fastq-piRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq" />
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273 <element name="reads-sample-small.fastq-piRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq" />
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274 <element name="reads-sample-small.fastq-piRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq" />
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275 <element name="reads-sample-small.fastq-piRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq" />
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276 <element name="reads-sample-small.fastq-siRNAs-genome" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq" />
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277 <element name="reads-sample-small.fastq-siRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq" />
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278 <element name="reads-sample-small.fastq-siRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq" />
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279 <element name="reads-sample-small.fastq-siRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq" />
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280 <element name="reads-sample-small.fastq-siRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq" />
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281 <element name="reads-sample-small.fastq-siRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq" />
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282 <element name="reads-sample-small.fastq_unique_mappers" file="fastq_dir/reads-sample-small.fastq_unique_mappers.fastq" />
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283 <element name="reads-sample-small.fastq_unmapped" file="fastq_dir/reads-sample-small.fastq_unmapped.fastq" />
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284 </output_collection>
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285 </test>
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286 </tests>
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287 <help>
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288 **User manual**
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289 "https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"
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290 </help>
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291 <citations>
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292 <citation type="doi">10.1186/s13100-018-0130-7</citation>
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293 </citations>
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294 </tool>