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1 <tool id="plant_microRNA_v1" name="miRPlant" veision="1.0.0">
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2 <description>tool for plant microRNA 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="2.11.0">R</requirement>
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8 <requirement type="package" version="0.0.13">fastx_toolkit </requirement>
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9 <requirement type="package" version="1.5">ViennaRNA</requirement>
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10 </requirements>
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11
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12 <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command-->
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13
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14 <command interpreter="perl">miRPlant.pl
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15 ## Change this to accommodate the number of threads you have available.
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16 -t \${GALAXY_SLOTS:-4}
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17 ## Do or not delet rfam mapped tags
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18 #if $params.delet_rfam == "yes":
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19 -D
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20 #end if
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21 -path \$SCRIPT_PATH
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22
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23 #for $j, $s in enumerate( $series )
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24 ##rank_of_series=$j
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25 -i ${s.input}
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26 -tag ${s.tag}
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27 #end for
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28
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29 -format $format -gfa $gfa -pre $pre -mat $mat -rfam $rfam -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe
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30 </command>
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31
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32 <inputs>
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33
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34 <repeat name="series" title="Series">
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35 <param name="input" type="data" label="Raw data"/>
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36 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
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37 </repeat>
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38
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39 <conditional name="params">
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40 <param name="delet_rfam" type="select" label="delet rfam mapped reads">
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41 <option value="yes" selected="true">yes</option>
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42 <option value="no">no</option>
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43 </param>
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44 </conditional> <!-- params -->
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45
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46 <!--param name="input" format="tabular" type="data" label="input config file" /-->
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47
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48 <param name="format" type="select" lable="raw data format" multiple="false">
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49 <option value="fastq">Raw data is fastq. format</option>
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50 <option value="fasta">Raw data is fasta. format</option>
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51 </param>
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52
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53 <param name="gfa" type="data" label="genome sequence fasta file"/>
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54 <!--param type="data" name="index" label="genome sequence bowtie index"/-->
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55 <param name="mat" type="data" label="mature microRNA sequence file" />
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56 <param name="pre" type="data" label="precursor microRNA sequence fie" />
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57 <param name="rfam" type="data" label="rfam sequence file" />
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58 <!--param type="data" name="idx2" label="rfam sequence bowtie index " -->
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59 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
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60 <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" />
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61 <param name="min" type="integer" value="19" label="minimum microRNA length" />
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62 <param name="max" type="integer" value="28" label="maximum microRNA length" />
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63 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to precursors" />
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64 <param name="e" type="integer" value="2" label="number of nucleotides upstream of the mature sequence to consider" />
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65 <param name="f" type="integer" value="5" label="number of nucleotides downstream of the mature sequence to consider" />
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66 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
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67 <param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
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68 <param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" />
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69 <param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" />
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70 <param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" />
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71 <param name="thread" type="integer" value="1" label="number of threads" />
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72 </inputs>
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73
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74 <outputs>
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75 <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt"/>
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76 <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln"/>
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77 <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs"/>
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78 <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa"/>
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79 <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa"/>
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80 <data format="txt" name="novel microRNA prediction file" from_work_dir="miRPlant_out/known_microRNA_mature.fa"/>
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81 <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt"/>
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82 <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa"/>
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83 <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa"/>
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84 <data format="txt" name="analysis result" from_work_dir="miRPlant_out/result.html"/>
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85 </outputs>
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86
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87 <help>
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88
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89 </help>
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90 </tool>
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