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comparison ribowaltz_plot.xml @ 0:8e903cb3f919 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 20:30:20 +0000
parents
children e25d81465c23
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-1:000000000000 0:8e903cb3f919
1 <tool id="ribowaltz_plot" name="riboWaltz-plot" version="@VERSION@" profile="@PROFILE@">
2 <description>visual inspection of ribosome profiling data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro='requirements'/>
7 <expand macro='edam_ontology' />
8 <expand macro='xrefs'/>
9 <command detect_errors="exit_code"><![CDATA[
10 Rscript '${__tool_directory__}/ribowaltz_plot.R' -i '$input_rdata'
11 #import json
12 #if $rlength_distr.plot == 'yes':
13 #set params_rlength_distr = []
14 #silent $params_rlength_distr.append(
15 {"cl": int($rlength_distr.plot_options.cl), "multisamples": str($rlength_distr.plot_options.multisamples),
16 "plot_style": str($rlength_distr.plot_options.plot_style)})
17 --params_rlength_distr '#echo json.dumps($params_rlength_distr)#'
18 #end if
19 #if $rends_heat.plot == 'yes':
20 #set params_rends_heat = []
21 #silent $params_rends_heat.append(
22 {"cl": int($rends_heat.plot_options.cl), "utr5l": int($rends_heat.plot_options.utr5l),
23 "cdsl": int($rends_heat.plot_options.cdsl), "utr3l": int($rends_heat.plot_options.utr3l)})
24 --params_rends_heat '#echo json.dumps($params_rends_heat)#'
25 #end if
26 #if $region_psite:
27 --region_psite_plot
28 #end if
29 #if $trint_periodicity.plot == 'yes':
30 #set length_range = 'all'
31 #if $trint_periodicity.plot_options.length_range.filter == 'range':
32 #$length_range = str($trint_periodicity.plot_options.length_range.length_range_min) + ':' + str($trint_periodicity.plot_options.length_range.length_range_max)
33 #end if
34 #set params_trint_periodicity = []
35 #silent $params_trint_periodicity.append(
36 {"cl": int($trint_periodicity.plot_options.cl), "region": str($trint_periodicity.plot_options.region),
37 "length_range": $length_range})
38 --params_trint_periodicity '#echo json.dumps($params_trint_periodicity)#'
39 #end if
40 #if $metaplots.plot == 'yes':
41 #set length_range = 'all'
42 #if $metaplots.plot_options.length_range.filter == 'range':
43 #$length_range = str($metaplots.plot_options.length_range.length_range_min) + ':' + str($metaplots.plot_options.length_range.length_range_max)
44 #end if
45 #set params_metaplots = []
46 #silent $params_metaplots.append(
47 {"multisamples": str($metaplots.plot_options.multisamples), "plot_style": str($metaplots.plot_options.plot_style),
48 "length_range": $length_range, "frequency": bool($metaplots.plot_options.frequency),
49 "utr5l": int($metaplots.plot_options.utr5l), "cdsl": int($metaplots.plot_options.cdsl),
50 "utr3l": int($metaplots.plot_options.utr3l)})
51 --params_metaplots '#echo json.dumps($params_metaplots)#'
52 #end if
53 #if $codon_usage_psite.plot == 'yes':
54 #set params_codon_usage_psite = []
55 #silent $params_codon_usage_psite.append(
56 {"fastapath": str($codon_usage_psite.plot_options.fastapath), "frequency": bool($codon_usage_psite.plot_options.frequency),
57 "label_scatter": bool($codon_usage_psite.plot_options.label_scatter),
58 "label_number": int($codon_usage_psite.plot_options.label_number)})
59 --params_codon_usage_psite '#echo json.dumps($params_codon_usage_psite)#'
60 #end if
61 ]]></command>
62 <inputs>
63 <param name="input_rdata" type="data" format="rdata" label="RDATA file generated by riboWaltz tool"/>
64 <conditional name="rlength_distr">
65 <param name="plot" type="select" label="Include read length distribution plots?">
66 <option value="no">no</option>
67 <option value="yes">yes</option>
68 </param>
69 <when value="yes">
70 <section name="plot_options" title="Plot options">
71 <param name="cl" type="integer" value="100" min="1" max="100" label="Confidence level"/>
72 <param name="multisamples" type="select" label="How to handle multiple samples and replicates?">
73 <option value="separated">Separate plots</option>
74 <option value="average">Sinlge plot with mean signal</option>
75 </param>
76 <param name="plot_style" type="select" label="How to organize and display multiple bar plots??">
77 <option value="split">Separate plots</option>
78 <option value="dodged">Sinlge plot with mean signal</option>
79 </param>
80 </section>
81 </when>
82 <when value="no"/>
83 </conditional>
84 <conditional name="rends_heat">
85 <param name="plot" type="select" label="Inlcude plots about abundance reads extremities around start and stop codons?">
86 <option value="no">no</option>
87 <option value="yes">yes</option>
88 </param>
89 <when value="yes">
90 <section name="plot_options" title="Plot options">
91 <param name="cl" type="integer" value="95" min="1" max="100" label="Confidence level"/>
92 <param name="utr5l" type="integer" value="50" min="0" label="5' UTR region flanking the start codon"/>
93 <param name="cdsl" type="integer" value="50" min="0" label="CDS region flanking both the start and stop codon"/>
94 <param name="utr3l" type="integer" value="50" min="0" label="3' UTR region flanking the stop codon"/>
95 </section>
96 </when>
97 <when value="no"/>
98 </conditional>
99 <param name="region_psite" type="boolean" truevalue="1" falsevalue="0" checked="false"
100 label="Inlcude plots that show P-sites per region?"/>
101 <conditional name="trint_periodicity">
102 <param name="plot" type="select" label="Inlcude plots with Trinucleotide periodicity?">
103 <option value="no">no</option>
104 <option value="yes">yes</option>
105 </param>
106 <when value="yes">
107 <section name="plot_options" title="Plot options">
108 <param name="cl" type="integer" value="95" min="1" max="100" label="Confidence level"/>
109 <param name="region" type="select" label="Region(s) of the apartment to be analyzed">
110 <option value="all" selected="true">All</option>
111 <option value="5end">5' UTR</option>
112 <option value="3end">3' UTR</option>
113 </param>
114 <conditional name="length_range">
115 <param name="filter" type="select" label="Read length(s) to be included in the analysis">
116 <option value="all" selected="true">All</option>
117 <option value="range">based on read length ranges</option>
118 </param>
119 <when value="all" />
120 <when value="range">
121 <param name="length_range_min" value="1" type="integer" min="1"
122 label="Read lengths ranging from"/>
123 <param name="length_range_max" value="100" type="integer" min="1"
124 label="Read lengths ranging to"/>
125 </when>
126 </conditional>
127 </section>
128 </when>
129 <when value="no"/>
130 </conditional>
131 <conditional name="metaplots">
132 <param name="plot" type="select" label="Inlcude metaplots?">
133 <option value="no">no</option>
134 <option value="yes">yes</option>
135 </param>
136 <when value="yes">
137 <section name="plot_options" title="Plot options">
138 <param name="multisamples" type="select" label="How to handle multiple samples and replicates?">
139 <option value="separated">Separate plots</option>
140 <option value="average">Sinlge plot with mean signal</option>
141 <option value="sum">Sinlge plot with sum of the signal</option>
142 </param>
143 <param name="plot_style" type="select" label="How to organize and display multiple bar plots??">
144 <option value="split">Separate plots</option>
145 <option value="dodged">Sinlge plot with mean signal</option>
146 </param>
147 <conditional name="length_range">
148 <param name="filter" type="select" label="Read length(s) to be included in the analysis">
149 <option value="all" selected="true">All</option>
150 <option value="range">based on read length ranges</option>
151 </param>
152 <when value="all" />
153 <when value="range">
154 <param name="length_range_min" value="1" type="integer" min="1"
155 label="Read lengths ranging from"/>
156 <param name="length_range_max" value="100" type="integer" min="1"
157 label="Read lengths ranging to"/>
158 </when>
159 </conditional>
160 <param name="frequency" type="boolean" truevalue="1" falsevalue="0" checked="false"
161 label="Normalize the metaprofile(s) such that the area under the curve(s) is 1?"
162 help="If checked and if multisamples is set to average or sum, normalization is performed
163 before combining the signal from multiple samples"/>
164 <param name="utr5l" type="integer" value="50" min="0" label="5' UTR region flanking the start codon"/>
165 <param name="cdsl" type="integer" value="50" min="0" label="CDS region flanking both the start and stop codon"/>
166 <param name="utr3l" type="integer" value="25" min="0" label="3' UTR region flanking the stop codon"/>
167 </section>
168 </when>
169 <when value="no"/>
170 </conditional>
171 <conditional name="codon_usage_psite">
172 <param name="plot" type="select" label="Inlcude plots with codon usage?">
173 <option value="no">no</option>
174 <option value="yes">yes</option>
175 </param>
176 <when value="yes">
177 <section name="plot_options" title="Plot options">
178 <param name="fastapath" type="data" format="fasta" />
179 <param name="frequency" type="boolean" truevalue="1" falsevalue="0" checked="true"
180 label="normalize the 64 codon usage indexes for the corresponding codon frequencies in coding sequences?"/>
181 <param name="label_scatter" type="boolean" truevalue="1" falsevalue="0" checked="false"
182 label="Label the dots in the scatter plot?"
183 help=" This parameter is considered only if there exatcly two input samples"/>
184 <param name="label_number" type="integer" value="64" min="1" max="64" label="how many dots in the scatter plot should be labeled?"/>
185 </section>
186 </when>
187 <when value="no"/>
188 </conditional>
189 </inputs>
190 <outputs>
191 <collection name="out_plots" type="list" label="riboWaltz plots on ${on_string}">
192 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" format="pdf" directory="." visible="false"/>
193 </collection>
194 </outputs>
195 <tests>
196 <test expect_num_outputs="1">
197 <param name="input_rdata" value="rep1.rdata"/>
198 <param name="region_psite" value="1"/>
199 <conditional name="rlength_distr">
200 <param name="plot" value="yes"/>
201 </conditional>
202 <conditional name="rends_heat">
203 <param name="plot" value="yes"/>
204 </conditional>
205 <conditional name="trint_periodicity">
206 <param name="plot" value="yes"/>
207 </conditional>
208 <conditional name="metaplots">
209 <param name="plot" value="yes"/>
210 </conditional>
211 <output_collection name="out_plots" type="list">
212 <element name="metaplots">
213 <assert_contents>
214 <has_size value="9180" delta="100"/>
215 </assert_contents>
216 </element>
217 <element name="psites_per_region">
218 <assert_contents>
219 <has_size value="5187" delta="100"/>
220 </assert_contents>
221 </element>
222 <element name="read_ends_heatmap">
223 <assert_contents>
224 <has_size value="26327" delta="500"/>
225 </assert_contents>
226 </element>
227 <element name="read_lengths">
228 <assert_contents>
229 <has_size value="4877" delta="100"/>
230 </assert_contents>
231 </element>
232 <element name="trinucleotide_periodicity">
233 <assert_contents>
234 <has_size value="7730" delta="100"/>
235 </assert_contents>
236 </element>
237 </output_collection>
238 </test>
239 </tests>
240 <help><![CDATA[
241 Visual inspection of ribosome profiling data. More information can be found here: https://github.com/LabTranslationalArchitectomics/riboWaltz
242
243 **Inputs**
244
245 RDATA file generated by rioWaltz tool.
246
247 **Outputs**
248
249 Generates various plots to visualize P-site offsets, codon usage etc.
250
251 ]]></help>
252 <expand macro="citations" />
253 </tool>