Mercurial > repos > iuc > ribowaltz_process

annotate ribowaltz.xml @ 1:042cab870a39 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
author iuc
date Mon, 23 Oct 2023 12:10:31 +0000
parents 6d4c94373bba
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042cab870a39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
iuc
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1 <tool id="ribowaltz_process" name="riboWaltz" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>calculation of optimal P-site offsets and diagnostic analysis</description>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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3 <macros>
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4 <import>macros.xml</import>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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5 </macros>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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6 <expand macro='edam_ontology' />
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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7 <expand macro='xrefs'/>
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042cab870a39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
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8 <expand macro='requirements'/>
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9 <command detect_errors="exit_code"><![CDATA[
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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10 #for $i, $sample in enumerate($rep_samples):
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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11 ln -s $sample.bam_file $sample.sample_name'.bam' &&
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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12 #end for
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042cab870a39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
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13 Rscript '${__tool_directory__}/ribowaltz.R' -b . -g '$gtf' --refseq_sep '$refseq_sep' --indel_threshold $indel_threshold
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6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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14 #import json
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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15 #if $filtering.duplicates.filter == 'yes':
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16 #set params_duplicate_filterting = []
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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17 #silent $params_duplicate_filterting.append({"extremity": str($filtering.duplicates.extremity), "keep": str($filtering.duplicates.keep)})
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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18 --params_duplicate_filterting '#echo json.dumps($params_duplicate_filterting)#'
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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19 #end if
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20 #if $filtering.length.filter == 'periodicity':
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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21 #set params_peridiocity_filterting = []
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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22 #silent $params_peridiocity_filterting.append({"periodicity_threshold": int($filtering.length.periodicity_threshold)})
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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23 --params_peridiocity_filterting '#echo json.dumps($params_peridiocity_filterting)#'
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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24 #end if
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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25 #if $filtering.length.filter == 'custom':
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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26 #set params_custom_filterting = []
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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27 #silent $params_custom_filterting.append({"length_range": str($filtering.length.length_range_min)+":"+str($filtering.length.length_range_max)})
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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28 --params_custom_filterting '#echo json.dumps($params_custom_filterting)#'
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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29 #end if
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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30 #set params_psite_additional = []
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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31 #silent $params_psite_additional.append(
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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32 {"flanking":int($psite_additional.flanking), "use_start":bool($psite_additional.use_start),
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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33 "psite_extrimity":str($psite_additional.psite_extrimity), "cl":int($psite_additional.cl)})
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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34 --params_psite_additional '#echo json.dumps($params_psite_additional)#'
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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35 #set params_coverage_additional = []
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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36 #silent $params_coverage_additional.append(
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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37 {"psites_per_region":bool($coverage_additional.psites_per_region), "min_overlap":int($coverage_additional.min_overlap),
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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38 "start_nts":int($coverage_additional.start_nts), "stop_nts":int($coverage_additional.stop_nts)})
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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39 --params_coverage_additional '#echo json.dumps($params_coverage_additional)#'
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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40 #if $save_rdata:
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41 --psite_info_rdata '$psite_rdata_out'
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42 #end if
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43 --codon_coverage_info '$codon_coverage_out'
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44 --cds_coverage_info '$cds_coverage_out' &&
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45 cd plots &&
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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46 for i in */*.pdf; do mv \$i \${i/\//-}; done;
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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47 ]]></command>
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48 <inputs>
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49 <repeat name="rep_samples" title="BAM file" min="1" default="1">
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50 <param name="sample_name" type="text" value="SampleName" label="Specify sample name"
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51 help="Only letters, numbers and underscores will be retained in this field">
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52 <sanitizer>
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53 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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54 </sanitizer>
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55 </param>
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56 <param name="bam_file" type="data" format="bam,sam" multiple="false" label="Input BAM file"
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57 help="riboWaltz only works for read alignments based on transcript coordinates"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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58 </repeat>
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59 <param name="gtf" type="data" format="gtf,gff" label="Annotation in GTF format"/>
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60 <param name="refseq_sep" type="text" optional="true" label="Separator between reference sequences' name and additional information to discard"
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61 help=" All characters before the first occurrence of the specified separator are kept"/>
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042cab870a39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
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62 <param name="indel_threshold" type="integer" value="5" min="0"
042cab870a39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
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63 label="Positive integer value specifying the maximum number of indels allowed for each read."/>
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64 <param name="save_rdata" type="boolean" truevalue="1" falsevalue="0" checked="true"
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65 label="Save p-site info RDATA file?"
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66 help="Useful for advanced plotting using riboWaltz-plot tool"/>
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67 <section name="filtering" title="Filtering Options">
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68 <conditional name="duplicates">
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69 <param name="filter" type="select" label="Perform duplicate filtering?">
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70 <option value="yes">yes</option>
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71 <option value="no">no</option>
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72 </param>
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73 <when value="yes">
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74 <param name="extremity" type="select" label="Which reads should be considered duplicates?">
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75 <option value="both" selected="true">Share both the 5' extremity and the 3' extremity </option>
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76 <option value="5end">Share only the 5' extremity</option>
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77 <option value="3end">Share only the 3' extremity</option>
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78 </param>
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79 <param name="keep" type="select" label="Which read to keep if duplicates disply different lengths?"
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80 help="This parameter is considered only if one of 5' or 3' end extrimity was chosen">
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81 <option value="shortest" selected="true">Keep the shortest reads </option>
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82 <option value="longest">Keep the longest reads</option>
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83 </param>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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84 </when>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
85 <when value="no"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
86 </conditional>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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87 <conditional name="length">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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88 <param name="filter" type="select" label="Perform read length filtering">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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89 <option value="periodicity">yes, in periodicity mode</option>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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90 <option value="custom">yes, based on read length ranges</option>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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91 <option value="no">no</option>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
92 </param>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
93 <when value="periodicity">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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94 <param name="periodicity_threshold" type="integer" value="50" min="10" max="100"
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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95 label="Only read lengths satisfying this threshold are kept"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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96 </when>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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97 <when value="custom">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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98 <param name="length_range_min" value="1" type="integer" min="1"
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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99 label="Read lengths ranging from"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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100 <param name="length_range_max" value="100" type="integer" min="1"
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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101 label="Read lengths ranging to"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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102 </when>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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103 <when value="no"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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104 </conditional>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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105 </section>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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106 <section name="psite_additional" title="Additional options for P-site offset computation">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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107 <param name="flanking" type="integer" value="6" label="Min number of nucleotides that must flank the reference codon in both directions"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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108 <param name="use_start" type="boolean" truevalue="1" falsevalue="0" checked="true"
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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109 label="Use the translation initiation site as reference codon?"
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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110 help="If not checked, the second to last codon is used instead"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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111 <param name="psite_extrimity" type="select" label="On which extrimity the correction step should be based on?">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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112 <option value="auto" selected="true">Automatically select the optimal extremity</option>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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113 <option value="5end">Use 5' extrimities</option>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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114 <option value="3end">Use 3' extrimities</option>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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115 </param>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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116 <param name="cl" type="integer" value="99" min="1" max="100"
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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117 label="Confidence level for generating occupancy metaprofiles for to a sub-range of read lengths"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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118 </section>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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119 <section name="coverage_additional" title="Options for codon and CDS coverage">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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120 <param name="psites_per_region" type="boolean" truevalue="1" falsevalue="0" checked="true"
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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121 label="Write number of P-Sites falling per region?"
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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122 help="If not checked, number of read foot prints per region trturned"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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123 <param name="min_overlap" type="integer" value="1" min="1" label="Min number of overlapping positions between reads and codons to be considered"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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124 <param name="start_nts" type="integer" value="0" min="0" label="Numer of nucleotides at the beginning of the coding sequences to be excluded"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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125 <param name="stop_nts" type="integer" value="0" min="0" label="Numer of nucleotides at the end of the coding sequences to be excluded"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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126 </section>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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127 </inputs>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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128 <outputs>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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129 <collection name="psite_out" type="list" label="P-site offsets information on ${on_string}">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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130 <discover_datasets pattern="(?P&lt;designation&gt;.+)_psite_info\.tsv" format="tabular" directory="." visible="false"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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131 </collection>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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132 <collection name="basic_plots" type="list:list" label="Ribosome occupancy profiles by read length on ${on_string}">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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133 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^-]+)-(?P&lt;identifier_1&gt;[^-]+)\.pdf" format="pdf" directory="plots/" visible="false"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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134 </collection>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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135 <data name="codon_coverage_out" format="tabular" label="Codon coverage on ${on_string}"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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136 <data name="cds_coverage_out" format="tabular" label="CDS coverage on ${on_string}"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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137 <data name="psite_rdata_out" format="rdata" label="Psite offset R object ${on_string}">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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138 <filter>save_rdata</filter>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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139 </data>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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140 </outputs>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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141 <tests>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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142 <test expect_num_outputs="5">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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143 <param name="gtf" value="rep1_annot.gtf.gz"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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144 <param name="refseq_sep" value="."/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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145 <param name="save_rdata" value="true"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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146 <repeat name="rep_samples">
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iuc
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147 <param name="sample_name" value="Replicate1"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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148 <param name="bam_file" value="rep1.bam"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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149 </repeat>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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150 <section name="filtering"/>
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iuc
parents:
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151 <section name="psite_additional">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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152 <param name="flanking" value="6"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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153 <param name="use_start" value="true"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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154 <param name="psite_extrimity" value="auto"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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155 <param name="cl" value="99"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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156 </section>
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iuc
parents:
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157 <section name="coverage_additional">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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158 <param name="psites_per_region" value="true"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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159 <param name="min_overlap" value="1"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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160 <param name="start_nts" value="0"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
161 <param name="stop_nts" value="0"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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162 </section>
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iuc
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163 <output_collection name="psite_out" type="list">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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164 <element name="Replicate1">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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165 <assert_contents>
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iuc
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166 <has_text_matching expression="transcript\tend5\tpsite\tend3\tlength\tcds_start\tcds_stop\tpsite_from_start\tpsite_from_stop\tpsite_region"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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167 <has_text_matching expression="ENSMUST00000015812\t1096\t1106\t1134\t39\t697\t1119\t409\t-13\tcds"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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168 </assert_contents>
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iuc
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169 </element>
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170 </output_collection>
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171 <output_collection name="basic_plots" type="list:list">
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172 <element name="Replicate1">
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173 <element name="21">
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174 <assert_contents>
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175 <has_size value="5501" delta="200"/>
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176 </assert_contents>
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177 </element>
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178 <element name="48">
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179 <assert_contents>
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180 <has_size value="6035" delta="200"/>
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181 </assert_contents>
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182 </element>
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183 </element>
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184 </output_collection>
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185 <output name="codon_coverage_out">
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186 <assert_contents>
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187 <has_text_matching expression="transcript\tstart\tend\tfrom_cds_start\tfrom_cds_stop\tregion\tReplicate1"/>
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188 <has_text_matching expression="ENSMUST00000000137\t2656\t2659\t865\t471\t3utr\t1"/>
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189 </assert_contents>
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190 </output>
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191 <output name="cds_coverage_out">
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192 <assert_contents>
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193 <has_text_matching expression="transcript\tlength_cds\tReplicate1"/>
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194 <has_text_matching expression="ENSMUST00000019109\t741\t5"/>
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195 </assert_contents>
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196 </output>
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197 <output name="psite_rdata_out">
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198 <assert_contents>
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199 <has_size value="171803" delta="1000"/>
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200 </assert_contents>
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201 </output>
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202 </test>
1
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203 <test expect_num_outputs="5">
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204 <param name="gtf" value="rep1_annot.gtf.gz"/>
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205 <param name="refseq_sep" value="."/>
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206 <param name="indel_threshold" value="3"/>
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207 <param name="save_rdata" value="true"/>
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208 <repeat name="rep_samples">
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209 <param name="sample_name" value="Replicate1"/>
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210 <param name="bam_file" value="rep1.bam"/>
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211 </repeat>
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212 <section name="filtering"/>
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213 <section name="psite_additional">
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214 <param name="flanking" value="3"/>
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215 <param name="use_start" value="true"/>
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216 <param name="psite_extrimity" value="auto"/>
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217 <param name="cl" value="99"/>
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218 </section>
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219 <section name="coverage_additional">
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220 <param name="psites_per_region" value="true"/>
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221 <param name="min_overlap" value="1"/>
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222 <param name="start_nts" value="0"/>
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223 <param name="stop_nts" value="0"/>
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224 </section>
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225 <output name="codon_coverage_out">
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226 <assert_contents>
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227 <has_text_matching expression="transcript\tstart\tend\tfrom_cds_start\tfrom_cds_stop\tregion\tReplicate1"/>
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228 <has_text_matching expression="ENSMUST00000000137\t2656\t2659\t865\t471\t3utr\t0"/>
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229 </assert_contents>
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230 </output>
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231 <output name="cds_coverage_out">
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232 <assert_contents>
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233 <has_text_matching expression="transcript\tlength_cds\tReplicate1"/>
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234 <has_text_matching expression="ENSMUST00000019109\t741\t5"/>
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235 </assert_contents>
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236 </output>
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237 <output name="psite_rdata_out">
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238 <assert_contents>
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239 <has_size value="169141" delta="1000"/>
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240 </assert_contents>
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241 </output>
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242 </test>
0
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243 </tests>
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244 <help><![CDATA[
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245 riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Taking advantage of a two-step algorithm where offset information is passed through populations of reads with different length in order to maximize offset coherence, riboWaltz computes with high precision the P-site offset. riboWaltz also provides a variety of graphical representations, laying the foundations for further accurate RiboSeq analyses and improved interpretation of positional information. More information can be found here: https://github.com/LabTranslationalArchitectomics/riboWaltz
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246
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247 **Inputs**
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248
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249 It takes BAM files and a GTF file as inputs. Most reads from RiboSeq are supposed to map on mRNAs and not on introns and intergenic regions. Hence, riboWaltz currently works for read alignments based on transcript coordinates. Reads should have been mapped to a reference *transcriptome*, NOT a reference genome.
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250
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251 **Outputs**
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252
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253 riboWaltz generates 4 outputs:
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254 * P-site offsets info: a collection containing P-site offsets information of each input sample.
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255 * Codon coverage: a tabular file containing the number of read footprints or P-sites mapping on each triplet of annotated coding sequences and UTRs.
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256 * CDS coverage: a tabular file containing the number of in-frame P-sites mapping on annotated coding sequence.
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257 * Plots: a collection containing plots of ribosome occupancy profiles based on the 5' and 3' extremity of reads mapping on the reference codon is generated for all samples and read lengths.
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258
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259 P-site offsets info file:
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260
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261 ====== ==========================================================
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262 Column Description
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263 ------ ----------------------------------------------------------
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264 1 transcript: the name of the corresponding reference sequence
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265 2 end5: its leftmost position with respect to the 1st nucleotide of the reference sequence
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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266 3 psite: the P-site position with respect to the 1st nucleotide of the transcript
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267 4 end3: its rightmost position with respect to the 1st nucleotide of the reference sequence
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268 5 length: length of the reference sequence
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269 6 cds_start: the leftmost position of the annotated CDS of the reference sequence (if any) with respect to its 1st nucleotide
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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270 7 cds_stop: the rightmost position of the annotated CDS of the reference sequence (if any) with respect to its 1st nucleotide
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271 8 psite_from_start: the P-site position with respect to the start codon of the annotated coding sequence (if any)
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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272 9 psite_from_stop: the P-site position with respect to the stop codon of the annotated coding sequence (if any)
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273 10 psite_region: the region of the transcript (5' UTR, CDS, 3' UTR) that includes the P-site
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274 ====== ==========================================================
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275
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276 Codon coverage:
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277
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278 ====== ==========================================================
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279 Column Description
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280 ------ ----------------------------------------------------------
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281 1 transcript: the name of the corresponding reference sequence
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282 2 start: its leftmost position with respect to the 1st nucleotide of the reference sequence
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283 3 end: its rightmost position with respect to the 1st nucleotide of the reference sequence
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284 4 from_cds_start: its position with respect to the first codon of the annotated CDS of the reference sequence
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285 5 from_cds_stop: its position with respect to the last codon of the annotated CDS of the reference sequence
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286 6 region: the region of the transcript (5' UTR, CDS, 3' UTR) it is in
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287 7-end the number of read footprints or P-sites falling in that region for each samples
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288 ====== ==========================================================
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289
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290 CDS coverage:
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291
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292 ====== ==========================================================
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293 Column Description
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294 ------ ----------------------------------------------------------
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295 1 transcript: the name of the corresponding reference sequence
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296 2 length_cds: length of the reference sequence
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297 3-end Number of in-frame P-sites mapping on its annotated coding region for each sample
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298 ====== ==========================================================
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299
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300 ]]></help>
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301 <expand macro="citations" />
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302 </tool>