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annotate pipmir.xml @ 0:16209195224c draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
author rnateam
date Fri, 25 Nov 2016 09:38:28 -0500
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16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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1 <tool id="pipmir" name="PIPmiR PIPELINE" version="0.1.0">
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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2
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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3 <description>a method to identify novel plant miRNA</description>
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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4
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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5 <requirements>
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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6 <!-- conda dependency -->
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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7 <requirement type="package" version="1.1">pipmir</requirement>
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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8 <requirement type="package" version="324">ucsc-fatotwobit</requirement>
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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9 </requirements>
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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11 <command>
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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12 <![CDATA[
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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14 #if $refGenomeSource.genomeSource == "history":
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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15 faToTwoBit '$refGenomeSource.ownFile' ownFile.2bit
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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16 &&
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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17 #end if
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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19 samtools sort
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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21 ## output in BAM format
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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22 -O BAM
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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24 ## output file name
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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25 -o test_sorted.bam
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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27 '$input_bam'
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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29 &&
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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30 samtools index test_sorted.bam test_sorted.bai
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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31
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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32 ## the tool requires the location of RNAfold binary
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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33 &&
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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34 RNAfold_location=\$(which RNAfold)
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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36 &&
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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37 PIPmiR PIPELINE
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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39 -a test_sorted.bam
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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40
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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41 ## genome source
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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42 #if $refGenomeSource.genomeSource == "history":
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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43 -t ownFile.2bit
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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44 #else
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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45 -t '$refGenomeSource.builtin.fields.path'
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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46 #end if
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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47
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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48 -o test
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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49
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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50 ## optional parameters
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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51 #if $params.settingsType == "custom":
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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52 ## default: 50
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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53 -l $params.min_precursor
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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54
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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55 ## default: 500
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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56 -L $params.max_precursor
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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57
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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58 ## default: 2
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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59 -s $params.step_size
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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60
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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61 ## default: 10
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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62 -m $params.min_read
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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63 #end if
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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64
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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65 ## default: 1
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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66 -p \${GALAXY_SLOTS:-1}
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67
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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68 -R \$RNAfold_location
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69
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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70 ]]>
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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71 </command>
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72 <inputs>
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73 <param name="input_bam" type="data"
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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74 format="sam,bam" label="Alignment"
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75 help="The bam or sam file containing alignment of the read data."/>
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76
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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77 <!-- Genome source. -->
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78 <conditional name="refGenomeSource">
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79 <param name="genomeSource" type="select"
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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80 label="Will you select a reference genome from your
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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81 history or use a built-in genome?"
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82 help="The version of genome against which the reads were aligned.">
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83 <option value="2bit" selected="True">
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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84 Use a built-in genome</option>
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85 <option value="history">
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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86 Use a genome from my current history</option>
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87 </param>
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88 <when value="2bit">
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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89 <param name="builtin" type="select"
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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90 label="Select a reference genome">
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91 <options from_data_table="lastz_seqs">
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
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92 <filter type="sort_by" column="1" />
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93 <validator type="no_options"
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94 message="A built-in reference genome is not available
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95 for the build associated with the selected input file"/>
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96 </options>
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97 </param>
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98 </when>
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99 <when value="history">
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100 <param name="ownFile" type="data" format="fasta"
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101 label="Select the reference genome" />
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102 </when>
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103 </conditional>
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104
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105 <!-- optional parameters -->
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106 <conditional name="params">
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107 <param name="settingsType" type="select"
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108 label="Optional parameters"
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109 help="You can use the default settings or
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110 set custom values for any of pipmir's parameters.">
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111 <option value="default">Use defaults</option>
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112 <option value="custom">Full parameter list</option>
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113 </param>
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114 <when value="default" />
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115 <!-- Full/advanced params. -->
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116 <when value="custom">
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117 <param name="min_precursor" type="integer"
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118 value="50" label="Minimum size"
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119 help="Minimum size of a precursor sequence (Default: 50)">
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120 <validator type="in_range"
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121 message="Minimum allowed value is 1" min="1"/>
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122 </param>
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123
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124 <param name="max_precursor" type="integer"
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125 value="500" label="Maximum size"
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126 help="Maximum size of a precursor sequence (Default: 500)">
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127 <validator type="in_range"
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128 message="Minimum allowed value is 1" min="1"/>
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129 </param>
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130
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131 <param name="step_size" type="integer"
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132 value="2" label="Step size"
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133 help="The step size used to identifiy the precursor
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134 from the minimum to the maximum possible
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135 size of precursor (Default: 2)">
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136 <validator type="in_range"
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137 message="Minimum allowed value is 1" min="1"/>
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138 </param>
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139
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140 <param name="min_read" type="integer"
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141 value="10" label="Minimum read count"
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142 help="Minimum read count for a mature to be
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143 considered expressed (Default: 10)">
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144 <validator type="in_range"
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145 message="Minimum allowed value is 1" min="1"/>
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146 </param>
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147 </when> <!-- full -->
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148 </conditional>
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149 </inputs>
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150 <outputs>
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151 <data name="putativeMatures" format="bed"
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152 from_work_dir="test_putativeMatures.bed"
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153 label="${tool.name} on ${on_string}: putative mature miRNAs"/>
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154
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155 <data name="predictedPrecursors" format="txt"
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156 from_work_dir="test_predictedPrecursors.txt"
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157 label="${tool.name} on ${on_string}: predicted precursor"/>
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158
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159 <data name="predicted_miRNA" format="txt"
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160 from_work_dir="test_predicted_miRNAs.txt"
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161 label="${tool.name} on ${on_string}: predicted miRNAs"/>
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162 </outputs>
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163 <tests>
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164 <test>
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165 <param name="input_bam" value="Aligned.out.sam" ftype="sam" />
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166 <param name="genomeSource" value="history" />
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167 <param name="ownFile" value="test_seq.fa" />
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168 <param name="settingsType" value="custom" />
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169 <param name="step_size" value="10" />
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170 <output name="putativeMatures" file="test_putativeMatures.bed"
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171 ftype="bed"/>
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172 <output name="predictedPrecursors" file="test_predictedPrecursors.txt"
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173 ftype="txt"/>
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174 <output name="predicted_miRNA" file="test_predicted_miRNAs.txt"
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175 ftype="txt"/>
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176 </test>
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177 </tests>
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178 <help>
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179 <![CDATA[
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180 .. class:: infomark
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181
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182 **What it does**
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183
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184 `pipmir`_ is an algorithm to identify novel plant miRNA genes from a combination
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185 of deep sequencing data and genomic features.
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186
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187 .. _pipmir: https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/
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188
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189 .. class:: infomark
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190
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191 **Optional parameters**
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192
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193 Minimum size
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194 * The MINIMUM size the precursor predictor can search.
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195 * 50 is recommended (and is the default).
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196
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197 Maximum size
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198 * The MAXIMUM size the precursor predictor can search.
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199
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200 * The larger you make this, the longer PIPmiR will take as folding time is exponential with increased size.
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201
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202 * 500 is what was used in the manuscript and will include almost all currently known Arabidopsis Thaliana miRNAs.
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203
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204 * 300 is a limit that will include most known miRNAs and still have a reasonable search time.
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205
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206 Step size
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207 * The step size used to identify the precursor from the minimum to the maximum possible size of a precursor.
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208
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209 * Increasing this value will speed up the precursor prediction step but limit the number of possible precursor sequences.
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210
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211 * 2 is the default and is what was used in the manuscript, however 5 still works well enough, and is only slightly less accurate
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212
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213 .. class:: infomark
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214
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215 **Outputs**
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216
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217 A `bed`_ file of putative mature miRNAs
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218 * 'name' column = an arbitrary name given to the putative mature
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219 * 'score' column = the read count
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220
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221 .. _bed: https://genome.ucsc.edu/FAQ/FAQformat#format1
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222
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223 A text file of predicted precursors
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224 * Form: Chromosome,Strand,Precursor_Start,Precursor_End,Sequence,Fold_Structure,Normalized_Minimum_Free_Energy,Mature_miRNA_Location
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225
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226 * Chromosome = chromosome that the precursor is on
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227
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228 * Strand = strand that the precursor is on
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229
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230 * Precursor_Start = start nucleotide (1 based) of the precursor
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231
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232 * Precursor_End = last nucleotide (1 based, inclusive) of the precursor
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233
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234 * Sequence = sequence of the precursor
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235
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236 * Fold_Structure = dot-bracket notation of the precursor fold centroid secondary structure (generated from RNAfold -p -d2 -noLP -noPS)
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237
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238 * Normalized_Minimum_Free_Energy = minimum free energy of the centroid structure divided by the length of the sequence
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239
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240 * Mature_miRNA_location = name & location of the mature miRNA within the precursor sequence
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241
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242 A text file of predicted miRNAs
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243 * This file will contain the miRNAs that had a positive classifier score, meaning that PIPmiR believes that they may be novel miRNA genes.
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244
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245 * This file contains the genomic coordinates of the predicted precursor as well as for the mature and star sequences.
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246
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247 * The file also contains the precursor sequence and the dot-bracket notation of its secondary structure.
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248 ]]></help>
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249 <citations>
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250 <citation type="doi">10.1101/gr.123547.111</citation>
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251 </citations>
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252 </tool>