Mercurial > repos > rnateam > paralyzer

annotate paralyzer.xml @ 1:f880686a9194 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
author rnateam
date Wed, 23 Oct 2019 19:07:22 -0400
parents 4dbe81be8b81
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4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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1 <tool id="paralyzer" name="PARalyzer" version="1.5">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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2 <description>A method to map interaction sites between RNA-binding proteins
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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3 and their targets</description>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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4 <requirements>
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5 <!-- conda dependency -->
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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6 <requirement type="package" version="1.5">paralyzer</requirement>
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7 <requirement type="package" version="324">ucsc-fatotwobit</requirement>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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8 </requirements>
1
f880686a9194 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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9 <command detect_errors="aggressive"><![CDATA[
0
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10
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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11 #if $refGenomeSource.genomeSource == "history":
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12 faToTwoBit '$refGenomeSource.ownFile' ownFile.2bit
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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13 &&
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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14 #end if
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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16 ## execute paralyzer
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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17 ## note the 2nd argument is the memory parameter
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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18 ## the parameter can be override in job_conf.xml e.g.
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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19 ## <env id="_JAVA_OPTIONS">-Xmx12G</env>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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20 PARalyzer 2G $input_ini
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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21
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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22 ]]>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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23 </command>
1
f880686a9194 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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24 <configfiles>
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25 <configfile name="input_ini">
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26 ## genome source
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27 #if $refGenomeSource.genomeSource == "history":
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28 GENOME_2BIT_FILE=ownFile.2bit
f880686a9194 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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29 #else
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30 GENOME_2BIT_FILE=$refGenomeSource.builtin.fields.path
f880686a9194 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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31 #end if
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32
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33 SAM_FILE=$input_sam$collapse
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34
f880686a9194 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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35 #if $methods.choice == "ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL":
f880686a9194 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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36 ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL=$methods.max_num
f880686a9194 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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37 #else:
f880686a9194 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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38 $methods.choice
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39 #end if
f880686a9194 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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40
f880686a9194 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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41 #if $conversion.selection == "custom":
f880686a9194 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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42 CONVERSION=$conversion.character_from>$conversion.character_to
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43 #end if
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44
f880686a9194 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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45 ## required parameters
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46 #if $params.settingsType == "custom":
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47 BANDWIDTH=$params.BANDWIDTH
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48 MINIMUM_READ_COUNT_PER_GROUP=$params.min_read_group
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49 MINIMUM_READ_COUNT_PER_CLUSTER=$params.min_read_cluster
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50 MINIMUM_READ_COUNT_FOR_KDE=$params.min_read_kde
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51 MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=$params.min_read_cluster_inc
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52 MINIMUM_CLUSTER_SIZE=$params.min_cluster_size
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53 MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=$params.min_conv_loc_cluster
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54 MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=$params.min_conv_cluster
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55 MINIMUM_READ_LENGTH=$params.min_read_len
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56 MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=$params.max_num_conv_mis
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57 #end if
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58
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59 OUTPUT_DISTRIBUTIONS_FILE=out.distribution
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60 OUTPUT_GROUPS_FILE=out.groups
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61 OUTPUT_CLUSTERS_FILE=out.clusters
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62 </configfile>
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63 </configfiles>
0
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64 <inputs>
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65 <param name="input_sam" type="data"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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66 format="sam" label="Alignment"
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67 help="The sam file containing alignment of the read data."/>
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68
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69 <param name="collapse" type="boolean" truevalue="=COLLAPSED"
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70 falsevalue="" checked="True"
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71 label="Incorporate the read copy number"
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72 help="If reads were collapse before alignment and you want
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73 to incorporate the read copy number, please select Yes,
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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74 otherwise select No" />
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75
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76 <!-- Genome source. -->
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77 <conditional name="refGenomeSource">
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78 <param name="genomeSource" type="select"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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79 label="Will you select a reference genome from your
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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80 history or use a built-in genome?"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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81 help="The version of genome against which the reads were aligned.">
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82 <option value="2bit" selected="True">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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83 Use a built-in genome</option>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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84 <option value="history">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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85 Use a genome from my current history</option>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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86 </param>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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87 <when value="2bit">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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88 <param name="builtin" type="select"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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89 label="Select a reference genome">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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90 <options from_data_table="lastz_seqs">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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91 <filter type="sort_by" column="1" />
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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92 <validator type="no_options"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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93 message="A built-in reference genome is not available
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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94 for the build associated with the selected input file"/>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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95 </options>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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96 </param>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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97 </when>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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98 <when value="history">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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99 <param name="ownFile" type="data" format="fasta"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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100 label="Select the reference genome" />
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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101 </when>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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102 </conditional>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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103
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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104 <conditional name="methods">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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105 <param name="choice" type="select"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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106 label="Please select one of the approaches"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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107 help="">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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108 <option value="EXTEND_BY_READ">
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109 EXTEND_BY_READ
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110 </option>
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111 <option value="HAFFNER_APPROACH">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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112 HAFFNER_APPROACH
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113 </option>
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114 <option value="ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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115 ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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116 </option>
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117 </param>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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118 <when value="EXTEND_BY_READ" />
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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119 <when value="HAFFNER_APPROACH" />
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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120 <when value="ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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121 <param name="max_num" type="integer"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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122 value="0" label="The maximum number"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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123 help="
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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124 The maximum number of reads to extend beyond the positive
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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125 signal in each direction (default 0) the cluster is defined
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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126 ">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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127 <validator type="in_range"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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128 message="Minimum allowed value is 0" min="0"/>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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129 </param>
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130 </when>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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131 </conditional>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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132
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133 <conditional name="conversion">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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134 <param name="selection" type="select"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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135 label="Conversion"
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136 help="Please specify characters">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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137 <option value="default">Use defaults: T to C</option>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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138 <option value="custom">Specify other characters</option>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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139 </param>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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140 <when value="default" />
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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141 <when value="custom">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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142 <param name="character_from" type="text"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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143 size="1" value="T" label="Character from"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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144 help="Character representing the modified ribonucleotide
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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145 (default 'T')">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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146 </param>
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147 <param name="character_to" type="text"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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148 size="1" value="C" label="Character to"
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149 help="Character representing what the modified ribonucleotide
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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150 is read as by rTranscriptase (default 'C')">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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151 </param>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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152 </when>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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153 </conditional>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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154
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155 <!-- optional parameters -->
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156 <conditional name="params">
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157 <param name="settingsType" type="select"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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158 label="Required parameters"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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159 help="You can use the default settings or
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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160 set custom values for any of paralyzer's parameters.">
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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161 <option value="default">Use defaults</option>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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162 <option value="custom">Full parameter list</option>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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163 </param>
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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164 <when value="default" />
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165 <!-- Full/advanced params. -->
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166 <when value="custom">
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167 <param name="BANDWIDTH" type="integer"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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168 value="3" label="BANDWIDTH"
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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169 help="Size of bandwidth for KDE calculation (default 3)">
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170 <validator type="in_range"
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171 message="Minimum allowed value is 1" min="1"/>
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172 </param>
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173
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174 <param name="min_read_group" type="integer"
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175 value="5" label="MINIMUM_READ_COUNT_PER_GROUP"
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176 help="Minimum number of reads required to call a group (default 5)">
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177 <validator type="in_range"
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178 message="Minimum allowed value is 1" min="1"/>
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179 </param>
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180
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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181 <param name="min_read_cluster" type="integer"
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182 value="2" label="MINIMUM_READ_COUNT_PER_CLUSTER"
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183 help="Minimum number of reads required to call a cluster (default 2)">
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184 <validator type="in_range"
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185 message="Minimum allowed value is 1" min="1"/>
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186 </param>
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187
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188 <param name="min_read_kde" type="integer"
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189 value="3" label="MINIMUM_READ_COUNT_FOR_KDE"
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190 help="Minimum read depth at a location to
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191 make a KDE estimate (default 3)">
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192 <validator type="in_range"
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193 message="Minimum allowed value is 1" min="1"/>
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194 </param>
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195
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196 <param name="min_read_cluster_inc" type="integer"
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197 value="1" label="MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION"
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198 help="Minimum read depth for a location to be included
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199 within a cluster (default 1)">
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200 <validator type="in_range"
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201 message="Minimum allowed value is 1" min="1"/>
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202 </param>
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203
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204 <param name="min_cluster_size" type="integer"
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205 value="11" label="MINIMUM_CLUSTER_SIZE"
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206 help="Minimum length required for a cluster
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207 to be reported (default 11)">
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208 <validator type="in_range"
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209 message="Minimum allowed value is 1" min="1"/>
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210 </param>
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211
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212 <param name="min_conv_loc_cluster" type="integer"
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213 value="2" label="MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER"
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214 help="Minimum number of separate locations to have a
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215 reported conversion for a cluster to be
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216 reported (default 2)">
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217 <validator type="in_range"
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218 message="Minimum allowed value is 1" min="1"/>
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219 </param>
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220
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221 <param name="min_conv_cluster" type="integer"
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222 value="2" label="MINIMUM_CONVERSION_COUNT_FOR_CLUSTER"
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223 help="Minimum number of conversion events within a
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224 region to report a cluster (default 2)">
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225 <validator type="in_range"
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226 message="Minimum allowed value is 1" min="1"/>
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227 </param>
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228
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229 <param name="min_read_len" type="integer"
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230 value="20" label="MINIMUM_READ_LENGTH"
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231 help="Minimum length of mapped read to be included
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232 in the analysis (default 20)">
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233 <validator type="in_range"
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234 message="Minimum allowed value is 1" min="1"/>
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235 </param>
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236
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237 <param name="max_num_conv_mis" type="integer"
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238 value="1" label="MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES"
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239 help="Maximum number of non-conversion mismatches of
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240 a mapped read to be included in the analysis (default 1)">
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241 <validator type="in_range"
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242 message="Minimum allowed value is 1" min="1"/>
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243 </param>
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244 </when> <!-- full -->
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245 </conditional>
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246 </inputs>
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247 <outputs>
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248 <data name="distribution" format="txt"
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249 from_work_dir="out.distribution"
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250 label="${tool.name} on ${on_string}: DISTRIBUTIONS"/>
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251
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252 <data name="groups" format="txt"
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253 from_work_dir="out.groups"
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254 label="${tool.name} on ${on_string}: GROUPS"/>
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255
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256 <data name="clusters" format="txt"
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257 from_work_dir="out.clusters"
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258 label="${tool.name} on ${on_string}: CLUSTERS"/>
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259
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260 <!--
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261 <data name="PARalyzer_Utilized" format="sam"
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262 from_work_dir="out_PARalyzer_Utilized.sam"
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263 label="${tool.name} on ${on_string}: PARalyzer_Utilized.sam"/>
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264 -->
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265 </outputs>
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266 <tests>
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267 <test>
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268 <param name="input_sam" value="input.sam" ftype="sam" />
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269 <param name="genomeSource" value="history" />
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270 <param name="ownFile" value="input.fa" />
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271 <param name="choice" value="EXTEND_BY_READ" />
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272 <param name="selection" value="custom" />
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273 <param name="character_from" value="T" />
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274 <param name="character_to" value="C" />
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275 <param name="settingsType" value="custom" />
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276 <param name="$BANDWIDTH" value="3" />
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277 <param name="min_read_group" value="5" />
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278 <param name="min_read_cluster" value="2" />
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279 <param name="min_read_kde" value="3" />
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280 <param name="min_read_cluster_inc" value="1" />
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281 <param name="min_cluster_size" value="11" />
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282 <param name="min_conv_loc_cluster" value="2" />
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283 <param name="min_conv_cluster" value="2" />
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284 <param name="min_read_len" value="20" />
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285 <param name="max_num_conv_mis" value="1" />
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286 <output name="distribution" file="out.distribution"
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287 ftype="txt"/>
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288 <output name="groups" file="out.groups"
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289 ftype="txt"/>
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290 <output name="clusters" file="out.clusters"
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291 ftype="txt"/>
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292 <!--
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293 <output name="PARalyzer_Utilized" file="out_PARalyzer_Utilized.sam"
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294 ftype="sam"/>
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295 -->
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296 </test>
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297 </tests>
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298 <help>
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299 <![CDATA[
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300 .. class:: infomark
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301
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302 **What it does**
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303
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304 `paralyzer`_ is an algorithm to generate a high resolution
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305 map of interaction sites between RNA-binding proteins and their targets. The
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306 algorithm utilizes the deep sequencing reads generated by `PAR-CLIP`_
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307 (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and
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308 Immunoprecipitation) protocol.The use of photoactivatable nucleotides in the
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309 PAR-CLIP protocol results in more efficient crosslinking between the
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310 RNA-binding protein and its target relative to other CLIP methods; in addition
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311 a nucleotide substitution occurs at the site of crosslinking, providing for
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312 single-nucleotide resolution binding information. PARalyzer utilizes this
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313 nucleotide substition in a kernel density estimate classifier to generate
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314 the high resolution set of Protein-RNA interaction sites.
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315
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316 .. _paralyzer: https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/
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317 .. _PAR-CLIP: http://www.ncbi.nlm.nih.gov/pubmed/20371350
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318
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319 .. class:: infomark
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320
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321 **Approaches**
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322
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323 ``EXTEND_BY_READ``: including this line means that the cluster will be extended
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324 beyond the signal to include a region such that it extends to
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325 the end of any read that falls within the cluster and contained
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326 a conversion, or until the minimum read depth
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327 (MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION parameter) is no longer met
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328
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329 ``HAFNER_APPROACH``: identifies the location with the largest number of conversion
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330 events and extends the cluster up to
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331 ( parameter ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL)nt
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332 in each direction from that point, or until the minimum
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333 read depth (MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION parameter) is no longer met
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334
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335 ``ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL``: the maximum number of reads to
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336 extend beyond the positive signal in each direction (default 0)
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337 the cluster is defined as the region where the conversion KDE is above
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338 the background KDE and then extended up to #integer#, or until the minimum
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339 read depth (MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION parameter) is no longer met
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340
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341 .. class:: infomark
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342
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343 **Outputs**
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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344
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345 DISTRIBUTIONS: contains the signal KDE, background KDE, read count & conversion for all locations within each group
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346 * The data will be in blocks of four lines for each group
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347 * groups on the reverse strand do not need to be reversed; the values always equal nucleotdies from GroupStart to GroupEnd, regardless of Strand
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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348 * First Column = Chromosome = chromosome on which the group resides
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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349 * Second Column = Strand = orientation in which the group resides
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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350 * Third Column = GroupStart = beginning coordinate on the chromosome of the group
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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351 * Fourth Column = GroupEnd = ending coordinate on the chromosome of the group
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352 * Fifth Column = GroupID = unique ID for the group
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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353 * Sixth Column = Information = reports if the current line contains the Signal, Background, Conversion Percent, or ReadCount
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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354 * All nucleotides that do not have any possibility of having a conversion event are given a value of -1
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355 * All Subsequent Columns: the values for each nucleotide from GroupStart until GroupEnd
4dbe81be8b81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit 52c43a8b9958fc46ab0284638038e690f5a0da3a
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356
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357
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358 GROUPS: a comma separated file containing the information about the resulting groups
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359 * Chromosome = chromosome on which the group resides
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360 * Strand = orientation in which the group resides
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361 * GroupStart = beginning coordinate on the chromosome of the group
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362 * GroupEnd = ending coordinate on the chromosome of the group
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363 * GroupID = unique ID for the group
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364 * ReadCount = number of reads within the group
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365
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366 CLUSTERS: a comma separated file containing the information about the resulting clusters
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367 * Chromosome = chromosome on which the cluster resides
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368 * Strand = orientation in which the cluster resides
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369 * ClusterStart = beginning coordinate on the chromosome of the cluster
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370 * ClusterEnd = ending coordinate on the chromosome of the cluster
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371 * ClusterID = unique ID for the cluster
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372 * ClusterSequence = sequence of the cluster
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373 * ReadCount = number of reads that overlap the cluster by at least 1 nucleotide
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374 * ModeLocation = coordinate of the location with the highest signal / (signal + background) value
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375 * ModeScore = score of the highest signal / (signal + background) value
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376 * ConversionLocationCount = number of unique location where at least 1 conversion occurred
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377 * ConversionEventCount = total number of conversions that occurred within the cluster
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378 * NonConversionEventCount = total number of possible conversion events that did not occur
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379
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380 ]]></help>
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381 <citations>
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382 <citation type="doi">10.1186/gb-2011-12-8-r79</citation>
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383 </citations>
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384 </tool>