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1 <tool id="micrornas" name="microRNA" veision="1.0.0">
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2 <description>Plant microRNA analysis </description>
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3
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4 <requirements>
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5 <requirement type="package" version="0.0.13">fastx_toolkit </requirement>
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6 <requirement type="package" version="0.12.7">bowtie</requirement>
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7 <requirement type="set_environment">SCRIPT_PATH</requirement>
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8 <!--requirement type="package" version="3.0.1">R</requirement!-->
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9 <requirement type="package" version="2.59">SVG</requirement>
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10 <requirement type="package" version="2.1.8">ViennaRNA</requirement>
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11 </requirements>
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12
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13 <!--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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14
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15 <command interpreter="perl">microRNA.pl
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16 ## Change this to accommodate the number of threads you have available.
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17 -t \${GALAXY_SLOTS:-4}
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18 -path \$SCRIPT_PATH
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19
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20
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21 ## Do or not annotate known microRNAs
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22 #if $params.known_microRNA == "yes":
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23 -pre $pre -mat $mat
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24 #end if
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25
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26 ## prepare bowtie index
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27 #set index_path = ''
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28 #if str($reference_genome.source) == "history":
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29 bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
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30 #set index_path = 'genome'
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31 #else:
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32 #set index_path = $reference_genome.index.fields.path
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33 #end if
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34
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35
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36 -gfa ${index_path}.fa -idx $index_path -mis $mismatch -i $config -fa $reads -e $e -f $f -r $r -dis $dis -flank $flank -mfe $mfe > run.log
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37 </command>
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38
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39 <inputs>
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40
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41 <!-- reference genome -->
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42 <conditional name="reference_genome">
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43 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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44 <option value="indexed">Use a built-in index</option>
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45 <option value="history">Use one from the history</option>
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46 </param>
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47 <when value="indexed">
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48 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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49 <options from_data_table="bowtie_indexes">
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50 <filter type="sort_by" column="2"/>
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51 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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52 </options>
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53 </param>
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54 </when>
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55 <when value="history">
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56 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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57 </when>
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58 </conditional>
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59
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60 <conditional name="params">
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61 <param name="known_microRNA" type="select" label="Analysis known microRNAs(eg. from mirbase)">
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62 <option value="yes" selected="true">yes</option>
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63 <option value="no">no</option>
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64 </param>
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65 <when value="yes">
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66 <param name="mat" type="data" label="mature microRNA sequence file" />
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67 <param name="pre" type="data" label="precursor microRNA sequence fie" />
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68 </when>
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69 </conditional> <!-- params -->
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70
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71 <param name="config" type="data" label="Raw data configs file" />
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72 <param name="reads" type="data" label="Input Fasta. file of candidate microRNA sequence" />
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73
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74
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75 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
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76 <param name="e" type="integer" value="2" label="number of nucleotides upstream of the mature sequence to consider" />
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77 <param name="f" type="integer" value="5" label="number of nucleotides downstream of the mature sequence to consider" />
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78 <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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79 <param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" />
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80 <param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" />
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81 <param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" />
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82
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83 </inputs>
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84
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85 <outputs>
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86 <data format="txt" name="known microRNA express list" from_work_dir="miRNA_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list">
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87 <filter>(params['known_microRNA'] == 'Yes')</filter>
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88 </data>
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89 <data format="txt" name="known microRNA express alignment" from_work_dir="miRNA_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment">
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90 <filter>(params['known_microRNA'] == 'Yes')</filter>
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91 </data>
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92 <data format="txt" name="known microRNA moRs result" from_work_dir="miRNA_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result">
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93 <filter>(params['known_microRNA'] == 'Yes')</filter>
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94 </data>
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95 <data format="txt" name="known microRNA precursor file" from_work_dir="miRNA_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file">
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96 <filter>(params['known_microRNA'] == 'Yes')</filter>
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97 </data>
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98 <data format="txt" name="known microRNA mature file" from_work_dir="miRNA_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file">
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99 <filter>(params['known_microRNA'] == 'Yes')</filter>
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100 </data>
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101 <data format="txt" name="novel microRNA express list" from_work_dir="miRNA_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/>
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102 <data format="txt" name="novel microRNA precursor file" from_work_dir="miRNA_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/>
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103 <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRNA_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/>
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104 <data format="txt" name="non-microRNA sequence FASTA file" from_work_dir="miRNA_out/non_miRNA_reads.fa" label="${tool.name} on ${on_string}: Sequence FASTA file of non-microRNA tags"/>
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105
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106 </outputs>
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107
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108 <help>
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109
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110 </help>
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111 </tool>
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