Mercurial > repos > iuc > ribowaltz_plot

annotate ribowaltz_plot.xml @ 1:e25d81465c23 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
author iuc
date Mon, 23 Oct 2023 12:10:37 +0000
parents 8e903cb3f919
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e25d81465c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
iuc
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1 <tool id="ribowaltz_plot" name="riboWaltz-plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>visual inspection of ribosome profiling data</description>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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6 <expand macro='edam_ontology' />
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7 <expand macro='xrefs'/>
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e25d81465c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
iuc
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8 <expand macro='requirements'/>
0
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9 <command detect_errors="exit_code"><![CDATA[
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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10 Rscript '${__tool_directory__}/ribowaltz_plot.R' -i '$input_rdata'
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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11 #import json
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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12 #if $rlength_distr.plot == 'yes':
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13 #set params_rlength_distr = []
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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14 #silent $params_rlength_distr.append(
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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15 {"cl": int($rlength_distr.plot_options.cl), "multisamples": str($rlength_distr.plot_options.multisamples),
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16 "plot_style": str($rlength_distr.plot_options.plot_style)})
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17 --params_rlength_distr '#echo json.dumps($params_rlength_distr)#'
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18 #end if
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19 #if $rends_heat.plot == 'yes':
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20 #set params_rends_heat = []
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21 #silent $params_rends_heat.append(
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22 {"cl": int($rends_heat.plot_options.cl), "utr5l": int($rends_heat.plot_options.utr5l),
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23 "cdsl": int($rends_heat.plot_options.cdsl), "utr3l": int($rends_heat.plot_options.utr3l)})
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24 --params_rends_heat '#echo json.dumps($params_rends_heat)#'
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25 #end if
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26 #if $region_psite:
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27 --region_psite_plot
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28 #end if
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29 #if $trint_periodicity.plot == 'yes':
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30 #set length_range = 'all'
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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31 #if $trint_periodicity.plot_options.length_range.filter == 'range':
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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32 #$length_range = str($trint_periodicity.plot_options.length_range.length_range_min) + ':' + str($trint_periodicity.plot_options.length_range.length_range_max)
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33 #end if
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34 #set params_trint_periodicity = []
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35 #silent $params_trint_periodicity.append(
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36 {"cl": int($trint_periodicity.plot_options.cl), "region": str($trint_periodicity.plot_options.region),
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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37 "length_range": $length_range})
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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38 --params_trint_periodicity '#echo json.dumps($params_trint_periodicity)#'
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39 #end if
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40 #if $metaplots.plot == 'yes':
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41 #set length_range = 'all'
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42 #if $metaplots.plot_options.length_range.filter == 'range':
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43 #$length_range = str($metaplots.plot_options.length_range.length_range_min) + ':' + str($metaplots.plot_options.length_range.length_range_max)
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44 #end if
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45 #set params_metaplots = []
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46 #silent $params_metaplots.append(
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47 {"multisamples": str($metaplots.plot_options.multisamples), "plot_style": str($metaplots.plot_options.plot_style),
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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48 "length_range": $length_range, "frequency": bool($metaplots.plot_options.frequency),
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49 "utr5l": int($metaplots.plot_options.utr5l), "cdsl": int($metaplots.plot_options.cdsl),
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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50 "utr3l": int($metaplots.plot_options.utr3l)})
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51 --params_metaplots '#echo json.dumps($params_metaplots)#'
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52 #end if
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53 #if $codon_usage_psite.plot == 'yes':
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54 #set params_codon_usage_psite = []
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55 #silent $params_codon_usage_psite.append(
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56 {"fastapath": str($codon_usage_psite.plot_options.fastapath), "frequency": bool($codon_usage_psite.plot_options.frequency),
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57 "label_scatter": bool($codon_usage_psite.plot_options.label_scatter),
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58 "label_number": int($codon_usage_psite.plot_options.label_number)})
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59 --params_codon_usage_psite '#echo json.dumps($params_codon_usage_psite)#'
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60 #end if
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61 ]]></command>
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62 <inputs>
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63 <param name="input_rdata" type="data" format="rdata" label="RDATA file generated by riboWaltz tool"/>
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64 <conditional name="rlength_distr">
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65 <param name="plot" type="select" label="Include read length distribution plots?">
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66 <option value="no">no</option>
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67 <option value="yes">yes</option>
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68 </param>
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69 <when value="yes">
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70 <section name="plot_options" title="Plot options">
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71 <param name="cl" type="integer" value="100" min="1" max="100" label="Confidence level"/>
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72 <param name="multisamples" type="select" label="How to handle multiple samples and replicates?">
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73 <option value="separated">Separate plots</option>
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74 <option value="average">Sinlge plot with mean signal</option>
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75 </param>
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76 <param name="plot_style" type="select" label="How to organize and display multiple bar plots??">
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77 <option value="split">Separate plots</option>
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78 <option value="dodged">Sinlge plot with mean signal</option>
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79 </param>
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80 </section>
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81 </when>
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82 <when value="no"/>
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83 </conditional>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
84 <conditional name="rends_heat">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
85 <param name="plot" type="select" label="Inlcude plots about abundance reads extremities around start and stop codons?">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
86 <option value="no">no</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
87 <option value="yes">yes</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
88 </param>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
89 <when value="yes">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
90 <section name="plot_options" title="Plot options">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
91 <param name="cl" type="integer" value="95" min="1" max="100" label="Confidence level"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
92 <param name="utr5l" type="integer" value="50" min="0" label="5' UTR region flanking the start codon"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
93 <param name="cdsl" type="integer" value="50" min="0" label="CDS region flanking both the start and stop codon"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
94 <param name="utr3l" type="integer" value="50" min="0" label="3' UTR region flanking the stop codon"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
95 </section>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
96 </when>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
97 <when value="no"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
98 </conditional>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
99 <param name="region_psite" type="boolean" truevalue="1" falsevalue="0" checked="false"
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
100 label="Inlcude plots that show P-sites per region?"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
101 <conditional name="trint_periodicity">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
102 <param name="plot" type="select" label="Inlcude plots with Trinucleotide periodicity?">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
103 <option value="no">no</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
104 <option value="yes">yes</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
105 </param>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
106 <when value="yes">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
107 <section name="plot_options" title="Plot options">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
108 <param name="cl" type="integer" value="95" min="1" max="100" label="Confidence level"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
109 <param name="region" type="select" label="Region(s) of the apartment to be analyzed">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
110 <option value="all" selected="true">All</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
111 <option value="5end">5' UTR</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
112 <option value="3end">3' UTR</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
113 </param>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
114 <conditional name="length_range">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
115 <param name="filter" type="select" label="Read length(s) to be included in the analysis">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
116 <option value="all" selected="true">All</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
117 <option value="range">based on read length ranges</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
118 </param>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
119 <when value="all" />
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
120 <when value="range">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
121 <param name="length_range_min" value="1" type="integer" min="1"
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
122 label="Read lengths ranging from"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
123 <param name="length_range_max" value="100" type="integer" min="1"
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
124 label="Read lengths ranging to"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
125 </when>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
126 </conditional>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
127 </section>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
128 </when>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
129 <when value="no"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
130 </conditional>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
131 <conditional name="metaplots">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
132 <param name="plot" type="select" label="Inlcude metaplots?">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
133 <option value="no">no</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
134 <option value="yes">yes</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
135 </param>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
136 <when value="yes">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
137 <section name="plot_options" title="Plot options">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
138 <param name="multisamples" type="select" label="How to handle multiple samples and replicates?">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
139 <option value="separated">Separate plots</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
140 <option value="average">Sinlge plot with mean signal</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
141 <option value="sum">Sinlge plot with sum of the signal</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
142 </param>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
143 <param name="plot_style" type="select" label="How to organize and display multiple bar plots??">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
144 <option value="split">Separate plots</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
145 <option value="dodged">Sinlge plot with mean signal</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
146 </param>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
147 <conditional name="length_range">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
148 <param name="filter" type="select" label="Read length(s) to be included in the analysis">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
149 <option value="all" selected="true">All</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
150 <option value="range">based on read length ranges</option>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
151 </param>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
152 <when value="all" />
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
153 <when value="range">
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
154 <param name="length_range_min" value="1" type="integer" min="1"
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
155 label="Read lengths ranging from"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
156 <param name="length_range_max" value="100" type="integer" min="1"
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
157 label="Read lengths ranging to"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
158 </when>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
159 </conditional>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
160 <param name="frequency" type="boolean" truevalue="1" falsevalue="0" checked="false"
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
161 label="Normalize the metaprofile(s) such that the area under the curve(s) is 1?"
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
162 help="If checked and if multisamples is set to average or sum, normalization is performed
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
163 before combining the signal from multiple samples"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
164 <param name="utr5l" type="integer" value="50" min="0" label="5' UTR region flanking the start codon"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
165 <param name="cdsl" type="integer" value="50" min="0" label="CDS region flanking both the start and stop codon"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
166 <param name="utr3l" type="integer" value="25" min="0" label="3' UTR region flanking the stop codon"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
167 </section>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
168 </when>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
169 <when value="no"/>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
diff changeset
170 </conditional>
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
parents:
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171 <conditional name="codon_usage_psite">
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172 <param name="plot" type="select" label="Inlcude plots with codon usage?">
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173 <option value="no">no</option>
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174 <option value="yes">yes</option>
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175 </param>
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176 <when value="yes">
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177 <section name="plot_options" title="Plot options">
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178 <param name="fastapath" type="data" format="fasta" />
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179 <param name="frequency" type="boolean" truevalue="1" falsevalue="0" checked="true"
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180 label="normalize the 64 codon usage indexes for the corresponding codon frequencies in coding sequences?"/>
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181 <param name="label_scatter" type="boolean" truevalue="1" falsevalue="0" checked="false"
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182 label="Label the dots in the scatter plot?"
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183 help=" This parameter is considered only if there exatcly two input samples"/>
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184 <param name="label_number" type="integer" value="64" min="1" max="64" label="how many dots in the scatter plot should be labeled?"/>
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185 </section>
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186 </when>
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187 <when value="no"/>
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188 </conditional>
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189 </inputs>
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190 <outputs>
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191 <collection name="out_plots" type="list" label="riboWaltz plots on ${on_string}">
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192 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" format="pdf" directory="." visible="false"/>
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193 </collection>
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194 </outputs>
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195 <tests>
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196 <test expect_num_outputs="1">
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197 <param name="input_rdata" value="rep1.rdata"/>
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198 <param name="region_psite" value="1"/>
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199 <conditional name="rlength_distr">
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200 <param name="plot" value="yes"/>
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201 </conditional>
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202 <conditional name="rends_heat">
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203 <param name="plot" value="yes"/>
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204 </conditional>
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205 <conditional name="trint_periodicity">
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206 <param name="plot" value="yes"/>
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207 </conditional>
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208 <conditional name="metaplots">
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209 <param name="plot" value="yes"/>
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210 </conditional>
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211 <output_collection name="out_plots" type="list">
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212 <element name="metaplots">
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213 <assert_contents>
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214 <has_size value="9180" delta="100"/>
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215 </assert_contents>
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216 </element>
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217 <element name="psites_per_region">
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218 <assert_contents>
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219 <has_size value="5187" delta="100"/>
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220 </assert_contents>
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221 </element>
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222 <element name="read_ends_heatmap">
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223 <assert_contents>
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224 <has_size value="26327" delta="500"/>
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225 </assert_contents>
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226 </element>
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227 <element name="read_lengths">
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228 <assert_contents>
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229 <has_size value="4877" delta="100"/>
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230 </assert_contents>
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231 </element>
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232 <element name="trinucleotide_periodicity">
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233 <assert_contents>
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234 <has_size value="7730" delta="100"/>
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235 </assert_contents>
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236 </element>
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237 </output_collection>
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238 </test>
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239 </tests>
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240 <help><![CDATA[
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241 Visual inspection of ribosome profiling data. More information can be found here: https://github.com/LabTranslationalArchitectomics/riboWaltz
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242
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243 **Inputs**
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244
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245 RDATA file generated by rioWaltz tool.
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246
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247 **Outputs**
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248
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249 Generates various plots to visualize P-site offsets, codon usage etc.
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250
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251 ]]></help>
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252 <expand macro="citations" />
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253 </tool>