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1 <tool id="plant_sirna_v1" name="siRNA" veision="1.0.0">
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2 <description>tool for plant siRNA analisis</description>
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3
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4 <requirements>
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5 <requirement type="set_environment">SCRIPT_PATH</requirement>
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6 <requirement type="package" version="0.12.7">bowtie</requirement>
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7 <requirement type="package" version="3.0.1">R</requirement>
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8 <requirement type="package" version="1.20.0">degseq</requirement>
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9 <requirement type="package" version="0.0.13">fastx_toolkit </requirement>
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10 <requirement type="package" version="1.96">threads</requirement>
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11 <requirement type="package" version="1.06">Parallel-ForkManager</requirement>
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12 <requirement type="package" version="2.59">SVG</requirement>
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29
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13 <requirement type="package" version="1.4_001">Boost-Graph</requirement>
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18
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14 </requirements>
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15
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16 <command interpreter="perl">siRNA.pl
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17 ## Change this to accommodate the number of threads you have available.
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18 -t \${GALAXY_SLOTS:-4}
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19
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20 -path \$SCRIPT_PATH
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21
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22 #for $j, $s in enumerate( $series )
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23 ##rank_of_series=$j
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24 -i ${s.input}
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25 -tag ${s.tag}
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26 #end for
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27
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28 ## Do or not annotate siRNAs by function
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29 #if $params.function_anno == "yes":
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30 -nat $params.nat -repeat $params.repeat
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31 #end if
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32
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33 ## Do or not DEG
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34 #if $degseq.degseq_analysis == "yes" :
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35 -deg $degseq.deg
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36 #end if
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37
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38 -format $format -g $genome -f $gff -mis $mis -rfam $rfam -v $v -a $a -n $mapnt -d $d -p $p -l $l -cen $cen -span $span > run.log
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39
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40 </command>
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41
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42 <inputs>
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43
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44 <repeat name="series" title="Series">
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45 <param name="input" type="data" label="Raw data file"/>
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46 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
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47 </repeat>
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48
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49 <param name="format" type="select" lable="raw data format" multiple="false">
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50 <option value="fastq">Raw data is fastq. format</option>
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51 <option value="fasta">Raw data is fasta. format</option>
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52 </param>
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53
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54 <param name="genome" type="data" label="genome sequence fasta file"/>
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55 <!--param type="data" name="index" label="genome sequence bowtie index"/-->
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56 <param name="gff" type="data" label="gff file" />
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57 <param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
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58 <param name="rfam" type="data" label="rfam sequence file" />
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59 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
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60 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
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61 <param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
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62 <param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />
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63
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64 <param name="p" type="select" lable="cluster method" multiple="false">
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65 <option value="F">conventional</option>
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66 <option value="T">NIBLES</option>
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67 </param>
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68 <param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />
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69
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70
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71 <conditional name="params">
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72 <param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
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73 <option value="no" selected="true">no</option>
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74 <option value="yes">yes</option>
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75 </param>
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76 <when value="yes">
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77 <param name="nat" type="data" label="atural antisense transcripts file" />
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78 <param name="repeat" type="data" label="repeat information file out of Repeatmasker" />
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79 </when>
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80 </conditional> <!-- params -->
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81
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82 <param name="cen" type="data" label="centromere file input" />
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83 <param name="span" type="integer" value="50000" label="plot span" />
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84
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85 <conditional name="degseq">
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86 <param name="degseq_analysis" type="select" label="Do or not identify Difference Expression Clusters">
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87 <option value="no" selected="true">no</option>
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88 <option value="yes">yes</option>
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89 </param>
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90 <when value="yes">
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91 <param name="deg" type="data" label="file config of de sample" />
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92 </when>
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93 </conditional>
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94
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95 </inputs>
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96
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97 <outputs>
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98 <data format="txt" name="siRNA cluster" from_work_dir="cluster_runs/total.result" label="${tool.name} on ${on_string}: siRNA cluster"/>
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99 <data format="html" name="analysis result" from_work_dir="cluster_runs/result.html" label="${tool.name} on ${on_string}: analysis result"/>
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100
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101 </outputs>
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102
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103 <help>
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104
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105 </help>
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106 </tool>
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