Mercurial > repos > iuc > ribowaltz_process

annotate ribowaltz.xml @ 0:f68c851c9368 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
author iuc
date Thu, 22 Sep 2022 20:29:05 +0000
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0
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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1 <tool id="ribowaltz_process" name="riboWaltz" version="@VERSION@" profile="@PROFILE@">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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2 <description>calculation of optimal P-site offsets and diagnostic analysis</description>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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3 <macros>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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4 <import>macros.xml</import>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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5 </macros>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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6 <expand macro='requirements'/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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7 <expand macro='edam_ontology' />
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8 <expand macro='xrefs'/>
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9 <command detect_errors="exit_code"><![CDATA[
f68c851c9368 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):
f68c851c9368 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 $sample.sample_name'.bam' &&
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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12 #end for
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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13 Rscript '${__tool_directory__}/ribowaltz.R' -b . -g '$gtf' --refseq_sep '$refseq_sep'
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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14 #import json
f68c851c9368 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':
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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16 #set params_duplicate_filterting = []
f68c851c9368 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($filtering.duplicates.keep)})
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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18 --params_duplicate_filterting '#echo json.dumps($params_duplicate_filterting)#'
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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19 #end if
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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20 #if $filtering.length.filter == 'periodicity':
f68c851c9368 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 = []
f68c851c9368 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)})
f68c851c9368 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)#'
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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24 #end if
f68c851c9368 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':
f68c851c9368 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 = []
f68c851c9368 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($filtering.length.length_range_max)})
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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28 --params_custom_filterting '#echo json.dumps($params_custom_filterting)#'
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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29 #end if
f68c851c9368 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 = []
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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31 #silent $params_psite_additional.append(
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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32 {"flanking":int($psite_additional.flanking), "use_start":bool($psite_additional.use_start),
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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33 "psite_extrimity":str($psite_additional.psite_extrimity), "cl":int($psite_additional.cl)})
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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34 --params_psite_additional '#echo json.dumps($params_psite_additional)#'
f68c851c9368 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 = []
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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36 #silent $params_coverage_additional.append(
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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37 {"psites_per_region":bool($coverage_additional.psites_per_region), "min_overlap":int($coverage_additional.min_overlap),
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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38 "start_nts":int($coverage_additional.start_nts), "stop_nts":int($coverage_additional.stop_nts)})
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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39 --params_coverage_additional '#echo json.dumps($params_coverage_additional)#'
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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40 #if $save_rdata:
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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41 --psite_info_rdata '$psite_rdata_out'
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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42 #end if
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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43 --codon_coverage_info '$codon_coverage_out'
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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44 --cds_coverage_info '$cds_coverage_out' &&
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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45 cd plots &&
f68c851c9368 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;
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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47 ]]></command>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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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"
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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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>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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54 </sanitizer>
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55 </param>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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56 <param name="bam_file" type="data" format="bam,sam" multiple="false" label="Input BAM file"
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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57 help="riboWaltz only works for read alignments based on transcript coordinates"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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58 </repeat>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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59 <param name="gtf" type="data" format="gtf,gff" label="Annotation in GTF format"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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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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62 <param name="save_rdata" type="boolean" truevalue="1" falsevalue="0" checked="true"
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63 label="Save p-site info RDATA file?"
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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64 help="Useful for advanced plotting using riboWaltz-plot tool"/>
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65 <section name="filtering" title="Filtering Options">
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66 <conditional name="duplicates">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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67 <param name="filter" type="select" label="Perform duplicate filtering?">
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68 <option value="yes">yes</option>
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69 <option value="no">no</option>
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70 </param>
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71 <when value="yes">
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72 <param name="extremity" type="select" label="Which reads should be considered duplicates?">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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73 <option value="both" selected="true">Share both the 5' extremity and the 3' extremity </option>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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74 <option value="5end">Share only the 5' extremity</option>
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75 <option value="3end">Share only the 3' extremity</option>
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76 </param>
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77 <param name="keep" type="select" label="Which read to keep if duplicates disply different lengths?"
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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78 help="This parameter is considered only if one of 5' or 3' end extrimity was chosen">
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79 <option value="shortest" selected="true">Keep the shortest reads </option>
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80 <option value="longest">Keep the longest reads</option>
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81 </param>
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82 </when>
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83 <when value="no"/>
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84 </conditional>
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diff changeset
85 <conditional name="length">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
86 <param name="filter" type="select" label="Perform read length filtering">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
87 <option value="periodicity">yes, in periodicity mode</option>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
88 <option value="custom">yes, based on read length ranges</option>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
89 <option value="no">no</option>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
90 </param>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
91 <when value="periodicity">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
92 <param name="periodicity_threshold" type="integer" value="50" min="10" max="100"
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
93 label="Only read lengths satisfying this threshold are kept"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
94 </when>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
95 <when value="custom">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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96 <param name="length_range_min" value="1" type="integer" min="1"
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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97 label="Read lengths ranging from"/>
f68c851c9368 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_max" value="100" type="integer" min="1"
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
99 label="Read lengths ranging to"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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100 </when>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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101 <when value="no"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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102 </conditional>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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103 </section>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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104 <section name="psite_additional" title="Additional options for P-site offset computation">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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105 <param name="flanking" type="integer" value="6" label="Min number of nucleotides that must flank the reference codon in both directions"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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106 <param name="use_start" type="boolean" truevalue="1" falsevalue="0" checked="true"
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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107 label="Use the translation initiation site as reference codon?"
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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108 help="If not checked, the second to last codon is used instead"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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109 <param name="psite_extrimity" type="select" label="On which extrimity the correction step should be based on?">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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110 <option value="auto" selected="true">Automatically select the optimal extremity</option>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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111 <option value="5end">Use 5' extrimities</option>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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112 <option value="3end">Use 3' extrimities</option>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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113 </param>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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114 <param name="cl" type="integer" value="99" min="1" max="100"
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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115 label="Confidence level for generating occupancy metaprofiles for to a sub-range of read lengths"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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diff changeset
116 </section>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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117 <section name="coverage_additional" title="Options for codon and CDS coverage">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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118 <param name="psites_per_region" type="boolean" truevalue="1" falsevalue="0" checked="true"
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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119 label="Write number of P-Sites falling per region?"
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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120 help="If not checked, number of read foot prints per region trturned"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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121 <param name="min_overlap" type="integer" value="1" min="1" label="Min number of overlapping positions between reads and codons to be considered"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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122 <param name="start_nts" type="integer" value="0" min="0" label="Numer of nucleotides at the beginning of the coding sequences to be excluded"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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123 <param name="stop_nts" type="integer" value="0" min="0" label="Numer of nucleotides at the end of the coding sequences to be excluded"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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124 </section>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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125 </inputs>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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126 <outputs>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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127 <collection name="psite_out" type="list" label="P-site offsets information on ${on_string}">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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128 <discover_datasets pattern="(?P&lt;designation&gt;.+)_psite_info\.tsv" format="tabular" directory="." visible="false"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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129 </collection>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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130 <collection name="basic_plots" type="list:list" label="Ribosome occupancy profiles by read length on ${on_string}">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
131 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^-]+)-(?P&lt;identifier_1&gt;[^-]+)\.pdf" format="pdf" directory="plots/" visible="false"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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132 </collection>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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133 <data name="codon_coverage_out" format="tabular" label="Codon coverage on ${on_string}"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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134 <data name="cds_coverage_out" format="tabular" label="CDS coverage on ${on_string}"/>
f68c851c9368 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="psite_rdata_out" format="rdata" label="Psite offset R object ${on_string}">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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136 <filter>save_rdata</filter>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
137 </data>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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diff changeset
138 </outputs>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
139 <tests>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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140 <test expect_num_outputs="5">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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141 <param name="gtf" value="rep1_annot.gtf.gz"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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142 <param name="refseq_sep" value="."/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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143 <param name="save_rdata" value="true"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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144 <repeat name="rep_samples">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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145 <param name="sample_name" value="Replicate1"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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146 <param name="bam_file" value="rep1.bam"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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147 </repeat>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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148 <section name="filtering"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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149 <section name="psite_additional">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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150 <param name="flanking" value="6"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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151 <param name="use_start" value="true"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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152 <param name="psite_extrimity" value="auto"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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153 <param name="cl" value="99"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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154 </section>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
155 <section name="coverage_additional">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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156 <param name="psites_per_region" value="true"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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157 <param name="min_overlap" value="1"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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158 <param name="start_nts" value="0"/>
f68c851c9368 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="stop_nts" value="0"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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160 </section>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
161 <output_collection name="psite_out" type="list">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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162 <element name="Replicate1">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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163 <assert_contents>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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164 <has_text_matching expression="transcript\tend5\tpsite\tend3\tlength\tcds_start\tcds_stop\tpsite_from_start\tpsite_from_stop\tpsite_region"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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165 <has_text_matching expression="ENSMUST00000015812\t1096\t1106\t1134\t39\t697\t1119\t409\t-13\tcds"/>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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166 </assert_contents>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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167 </element>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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168 </output_collection>
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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169 <output_collection name="basic_plots" type="list:list">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
170 <element name="Replicate1">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
171 <element name="21">
f68c851c9368 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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172 <assert_contents>
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173 <has_size value="5501" delta="200"/>
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174 </assert_contents>
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175 </element>
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176 <element name="48">
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177 <assert_contents>
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178 <has_size value="6035" delta="200"/>
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179 </assert_contents>
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180 </element>
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181 </element>
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182 </output_collection>
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183 <output name="codon_coverage_out">
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184 <assert_contents>
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185 <has_text_matching expression="transcript\tstart\tend\tfrom_cds_start\tfrom_cds_stop\tregion\tReplicate1"/>
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186 <has_text_matching expression="ENSMUST00000000137\t2656\t2659\t865\t471\t3utr\t1"/>
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187 </assert_contents>
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188 </output>
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189 <output name="cds_coverage_out">
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190 <assert_contents>
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191 <has_text_matching expression="transcript\tlength_cds\tReplicate1"/>
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192 <has_text_matching expression="ENSMUST00000019109\t741\t5"/>
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193 </assert_contents>
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194 </output>
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195 <output name="psite_rdata_out">
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196 <assert_contents>
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197 <has_size value="171803" delta="1000"/>
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198 </assert_contents>
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199 </output>
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200 </test>
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201 </tests>
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202 <help><![CDATA[
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203 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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204
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205 **Inputs**
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206
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207 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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208
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209 **Outputs**
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210
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211 riboWaltz generates 4 outputs:
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212 * P-site offsets info: a collection containing P-site offsets information of each input sample.
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213 * 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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214 * CDS coverage: a tabular file containing the number of in-frame P-sites mapping on annotated coding sequence.
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215 * 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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216
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217 P-site offsets info file:
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218
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219 ====== ==========================================================
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220 Column Description
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221 ------ ----------------------------------------------------------
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222 1 transcript: the name of the corresponding reference sequence
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223 2 end5: its leftmost position with respect to the 1st nucleotide of the reference sequence
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224 3 psite: the P-site position with respect to the 1st nucleotide of the transcript
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225 4 end3: its rightmost position with respect to the 1st nucleotide of the reference sequence
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226 5 length: length of the reference sequence
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227 6 cds_start: the leftmost position of the annotated CDS of the reference sequence (if any) with respect to its 1st nucleotide
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228 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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229 8 psite_from_start: the P-site position with respect to the start codon of the annotated coding sequence (if any)
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230 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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231 10 psite_region: the region of the transcript (5' UTR, CDS, 3' UTR) that includes the P-site
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232 ====== ==========================================================
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233
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234 Codon coverage:
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235
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236 ====== ==========================================================
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237 Column Description
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238 ------ ----------------------------------------------------------
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239 1 transcript: the name of the corresponding reference sequence
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240 2 start: its leftmost position with respect to the 1st nucleotide of the reference sequence
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241 3 end: its rightmost position with respect to the 1st nucleotide of the reference sequence
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242 4 from_cds_start: its position with respect to the first codon of the annotated CDS of the reference sequence
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243 5 from_cds_stop: its position with respect to the last codon of the annotated CDS of the reference sequence
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244 6 region: the region of the transcript (5' UTR, CDS, 3' UTR) it is in
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245 7-end the number of read footprints or P-sites falling in that region for each samples
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246 ====== ==========================================================
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247
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248 CDS coverage:
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249
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250 ====== ==========================================================
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251 Column Description
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252 ------ ----------------------------------------------------------
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253 1 transcript: the name of the corresponding reference sequence
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254 2 length_cds: length of the reference sequence
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255 3-end Number of in-frame P-sites mapping on its annotated coding region for each sample
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256 ====== ==========================================================
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257
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258 ]]></help>
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259 <expand macro="citations" />
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260 </tool>