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1 <tool id="mirdeep2" name="miRDeep2">
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2 <description>Find miRNA candidates using output from mapping step</description>
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3
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4 <requirements>
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5 <requirement type="perl-module">mirdeep2_wrapper.pl</requirement>
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6 </requirements>
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7
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8 <command interpreter="perl">
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9 ./mirdeep2_wrapper.pl $collapsed_reads $bowtie_index $bowtie_index.extra_files_path $arf_file $mirna_ref $mirna_other $precursors "$html_output.files_path" "$collapsed_reads.name" $csv_output $html_output $survey_output $mrd_output
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10
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11 #if str($min_stack_height) != '':
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12 -a $min_stack_height
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13 #end if
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14
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15 #if str($max_num_precursors) != '':
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16 -g $max_num_precursors
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17 #end if
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18
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19 #if str($min_score_cutoff) != '':
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20 -b $min_score_cutoff
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21 #end if
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22
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23 #if str($disable_randfold) == 'disable_randfold_true':
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24 -c
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25 #end if
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26
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27 #if str($ucsc_genome) != 'None':
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28 -t $ucsc_genome
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29 #end if
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30
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31 #if str($star_seq) != 'None':
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32 -s $star_seq
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33 #end if
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34 </command>
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35
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36 <inputs>
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37 <param format="fasta" type="data" name="collapsed_reads" optional="false" label="Collapsed reads fasta file" help="Collapsed read fasta file outputted from mapping step"/>
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38
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39 <param format="bowtie_html_index" type="data" name="bowtie_index" optional="false" label="Bowtie indexed reference" help="Select the bowtie-build run, NOT the fasta reference file you indexed"/>
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40
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41 <param format="arf" type="data" name="arf_file" optional="false" label="ARF file from mapping step"/>
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42
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43 <param format="fasta" type="data" name="mirna_ref" optional="true" label="Known miRBase miRNA sequences in fasta format (optional)" help="If used, these should be the known mature sequences for the species being analyzed"/>
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44
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45 <param format="fasta" type="data" name="mirna_other" optional="true" label="Known related miRBase miRNA sequences in fasta format (optional)" help="If used, these should be pooled known mature sequences for 1-5 species closely related to the species being analyzed"/>
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46
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47 <param format="fasta" type="data" name="precursors" optional="true" label="Known miRBase miRNA precursors in fasta format (optional)" help="If used, these should be the known precursor sequences for the species being analyzed"/>
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48
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49 <param format="fasta" type="data" name="star_seq" optional="true" label="Known miRBase miRNA star sequences in fasta format (optional)" help="If used, these should be the known star sequences for the species being analyzed"/>
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50
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51 <param name="min_stack_height" value="" type="integer" optional="true" label="Minimum read stack height that triggers analysis (optional)" help="Using this option disables automatic estimation of the optimal value and all detected precursors are analyzed"/>
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52
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53 <param name="max_num_precursors" value="50000" type="integer" label="Maximum number of precursors to analyze when automatic excision gearing is used (default 50000)" help="If set to -1 all precursors will be analyzed"/>
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54
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55 <param name="min_score_cutoff" value="0" type="integer" label="Minimum score cut-off for predicted novel miRNAs to be displayed in the overview table" help="This score cut-off is by default 0"/>
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56
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57 <param name="disable_randfold" type="boolean" truevalue="disable_randfold_true" falsevalue="disable_randfold_false" checked="false" label="Disable randfold analysis" help="Runs faster but with less accurate results"/>
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58
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59 <param name="ucsc_genome" type="select" optional="true" label="Species being analyzed - this is used to link to the appropriate UCSC browser entry (optional)">
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60 <options from_file="ucsc_browser_species.txt">
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61 <column name="value" index="0"/>
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62 </options>
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63 </param>
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64 </inputs>
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65
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66 <outputs>
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67 <data format="csv" name="csv_output" label="miRNA CSV output of ${tool.name} on ${on_string}"/>
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68 <data format="html" name="html_output" label="miRNA HTML output of ${tool.name} on ${on_string}"/>
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69 <data format="csv" name="survey_output" label="miRNA prediction accuracy spreadsheet of ${tool.name} on ${on_string}"/>
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70 <data format="txt" name="mrd_output" label="miRNA hairpins of ${tool.name} on ${on_string}"/>
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71 </outputs>
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72
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73 <help>
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74 miRDeep2 is a software package for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples.
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75
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76 The output files produced are:
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77
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78 result.html: a html table giving an overview of novel and known miRNAs detected in the data. The table is hyperlinked to pdfs showing the signature and structure of each hairpin.
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79
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80 result.csv: spread-sheet format of results.html
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81
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82 survey.csv: spread-sheet of prediction accuracy for all score-cutoffs between -10 and 10.
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83
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84 output.mrd: text output of the reported hairpins.
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85
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86 </help>
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87 </tool>
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