Mercurial > repos > iuc > ribowaltz_process

annotate ribowaltz.xml @ 0:6d4c94373bba draft

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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 20:30:54 +0000
parents
children 042cab870a39
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6d4c94373bba 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@">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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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
iuc
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3 <macros>
6d4c94373bba 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>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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5 </macros>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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6 <expand macro='requirements'/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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7 <expand macro='edam_ontology' />
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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8 <expand macro='xrefs'/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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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
iuc
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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 $sample.sample_name'.bam' &&
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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12 #end for
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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13 Rscript '${__tool_directory__}/ribowaltz.R' -b . -g '$gtf' --refseq_sep '$refseq_sep'
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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14 #import json
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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15 #if $filtering.duplicates.filter == 'yes':
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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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
iuc
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17 #silent $params_duplicate_filterting.append({"extremity": str($filtering.duplicates.extremity), "keep": str($filtering.duplicates.keep)})
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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18 --params_duplicate_filterting '#echo json.dumps($params_duplicate_filterting)#'
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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19 #end if
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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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
iuc
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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
iuc
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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
iuc
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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
iuc
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24 #end if
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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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
iuc
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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
iuc
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27 #silent $params_custom_filterting.append({"length_range": str($filtering.length.length_range_min)+":"+str($filtering.length.length_range_max)})
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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28 --params_custom_filterting '#echo json.dumps($params_custom_filterting)#'
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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29 #end if
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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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
iuc
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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($psite_additional.use_start),
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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33 "psite_extrimity":str($psite_additional.psite_extrimity), "cl":int($psite_additional.cl)})
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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34 --params_psite_additional '#echo json.dumps($params_psite_additional)#'
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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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
iuc
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36 #silent $params_coverage_additional.append(
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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37 {"psites_per_region":bool($coverage_additional.psites_per_region), "min_overlap":int($coverage_additional.min_overlap),
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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38 "start_nts":int($coverage_additional.start_nts), "stop_nts":int($coverage_additional.stop_nts)})
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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39 --params_coverage_additional '#echo json.dumps($params_coverage_additional)#'
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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40 #if $save_rdata:
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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41 --psite_info_rdata '$psite_rdata_out'
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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42 #end if
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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43 --codon_coverage_info '$codon_coverage_out'
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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44 --cds_coverage_info '$cds_coverage_out' &&
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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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>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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48 <inputs>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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49 <repeat name="rep_samples" title="BAM file" min="1" default="1">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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50 <param name="sample_name" type="text" value="SampleName" label="Specify sample name"
6d4c94373bba 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">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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52 <sanitizer>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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53 <valid initial="string.letters,string.digits"><add value="_" /></valid>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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54 </sanitizer>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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55 </param>
6d4c94373bba 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"
6d4c94373bba 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"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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58 </repeat>
6d4c94373bba 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"/>
6d4c94373bba 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"
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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61 help=" All characters before the first occurrence of the specified separator are kept"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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62 <param name="save_rdata" 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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63 label="Save p-site info RDATA file?"
6d4c94373bba 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"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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65 <section name="filtering" title="Filtering Options">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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66 <conditional name="duplicates">
6d4c94373bba 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?">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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68 <option value="yes">yes</option>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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69 <option value="no">no</option>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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70 </param>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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71 <when value="yes">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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72 <param name="extremity" type="select" label="Which reads should be considered duplicates?">
6d4c94373bba 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>
6d4c94373bba 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>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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75 <option value="3end">Share only the 3' extremity</option>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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76 </param>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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77 <param name="keep" type="select" label="Which read to keep if duplicates disply different lengths?"
6d4c94373bba 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">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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79 <option value="shortest" selected="true">Keep the shortest reads </option>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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80 <option value="longest">Keep the longest reads</option>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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81 </param>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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82 </when>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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83 <when value="no"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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84 </conditional>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
85 <conditional name="length">
6d4c94373bba 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">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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87 <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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88 <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:
diff changeset
89 <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
90 </param>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
91 <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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92 <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:
diff changeset
93 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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94 </when>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
95 <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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96 <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
parents:
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97 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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98 <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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99 label="Read lengths ranging to"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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100 </when>
6d4c94373bba 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"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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102 </conditional>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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103 </section>
6d4c94373bba 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">
6d4c94373bba 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"/>
6d4c94373bba 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"
6d4c94373bba 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?"
6d4c94373bba 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"/>
6d4c94373bba 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?">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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110 <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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111 <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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112 <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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113 </param>
6d4c94373bba 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"
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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115 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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116 </section>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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117 <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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118 <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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119 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
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120 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
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"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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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"/>
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="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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124 </section>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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125 </inputs>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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126 <outputs>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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127 <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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128 <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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129 </collection>
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iuc
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130 <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
parents:
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131 <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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132 </collection>
6d4c94373bba 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}"/>
6d4c94373bba 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}"/>
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="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
parents:
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136 <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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137 </data>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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138 </outputs>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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139 <tests>
6d4c94373bba 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">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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141 <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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142 <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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143 <param name="save_rdata" 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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144 <repeat name="rep_samples">
6d4c94373bba 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"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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146 <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
parents:
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147 </repeat>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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148 <section name="filtering"/>
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iuc
parents:
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149 <section name="psite_additional">
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iuc
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150 <param name="flanking" value="6"/>
6d4c94373bba 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"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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152 <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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153 <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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154 </section>
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iuc
parents:
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155 <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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156 <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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157 <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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158 <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
159 <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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160 </section>
6d4c94373bba 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">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
162 <element name="Replicate1">
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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163 <assert_contents>
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iuc
parents:
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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"/>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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165 <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
parents:
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166 </assert_contents>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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167 </element>
6d4c94373bba 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>
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iuc
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169 <output_collection name="basic_plots" type="list:list">
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170 <element name="Replicate1">
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171 <element name="21">
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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
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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258 ]]></help>
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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259 <expand macro="citations" />
6d4c94373bba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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260 </tool>