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comparison hyphy_summary.xml @ 0:f304c108aa1f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author iuc
date Wed, 09 Jun 2021 07:03:54 +0000
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1 <?xml version="1.0"?>
2 <tool id="hyphy_summary" version="1.0.0" name="HyPhy-Summary" profile="21.01">
3 <description>generate summary report of HyPhy analyses</description>
4 <requirements>
5 <requirement type="package" version="0.19.7">python-bioext</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/scripts/hyphy_summary.py'
9 --mode $mode_conditional.mode
10 #if $mode_conditional.mode == 'summary':
11 --combined '$mode_conditional.combined'
12 --pvalue $mode_conditional.pvalue
13 --gene '$mode_conditional.gene'
14 --labels '$mode_conditional.labels'
15 --default-tag '$mode_conditional.default_tag'
16 --name '$mode_conditional.name'
17 #if $mode_conditional.relax:
18 --relax '$mode_conditional.relax'
19 #end if
20 #if $mode_conditional.busted:
21 --busted '$mode_conditional.busted'
22 #end if
23 #if $mode_conditional.slac:
24 --slac '$mode_conditional.slac'
25 #end if
26 #if $mode_conditional.fel:
27 --fel '$mode_conditional.fel'
28 #end if
29 #if $mode_conditional.cfel:
30 --cfel '$mode_conditional.cfel'
31 #end if
32 #if $mode_conditional.meme:
33 --meme '$mode_conditional.meme'
34 #end if
35 #if $mode_conditional.meme_full:
36 --meme-full '$mode_conditional.meme_full'
37 #end if
38 #if $mode_conditional.prime:
39 --prime '$mode_conditional.prime'
40 #end if
41 #if $mode_conditional.fade:
42 --fade '$mode_conditional.fade'
43 #end if
44 #if $mode_conditional.bgm:
45 --bgm '$mode_conditional.bgm'
46 #end if
47 #else:
48 --annotation-inputs '$mode_conditional.annotation_inputs'
49 --summary-inputs '$mode_conditional.summary_inputs'
50 #end if
51 --annotation-output '$annotation'
52 --summary-output '$summary'
53 ]]></command>
54 <inputs>
55 <conditional name="mode_conditional">
56 <param argument="--mode" type="select" label="Mode">
57 <option value="summary">Generate gene summary</option>
58 <option value="merge">Merge gene summaries for clade analysis</option>
59 </param>
60 <when value="summary">
61 <param argument="--combined" type="data" format="fasta" label="Combined reference and query alignments from TN93-Filter" />
62 <param argument="--pvalue" type="float" min="0" max="1" value="0.05" label="p-value to use" />
63 <param argument="--labels" type="data" format="json,hyphy_results.json" label="HyPhy-Annotate branche labels in JSON format" />
64 <param argument="--gene" type="text" label="Name of the gene or sequence being analyzed">
65 <sanitizer invalid_char="">
66 <valid initial="string.ascii_letters,string.digits">
67 <add value="_" />
68 <add value="-" />
69 </valid>
70 </sanitizer>
71 </param>
72 <param argument="--default-tag" type="text" value="Reference" label="Default name for sequences that have no explicit label">
73 <sanitizer invalid_char="">
74 <valid initial="string.ascii_letters,string.digits">
75 <add value="_" />
76 <add value="-" />
77 </valid>
78 </sanitizer>
79 </param>
80 <param argument="--name" type="text" label="The sequence ID to highlight">
81 <sanitizer invalid_char="">
82 <valid initial="string.ascii_letters,string.digits">
83 <add value="_" />
84 <add value="-" />
85 </valid>
86 </sanitizer>
87 </param>
88 <param argument="--fade" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-FADE output dataset" />
89 <param argument="--prime" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-PRIME output dataset" />
90 <param argument="--relax" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-RELAX output dataset" />
91 <param argument="--meme" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-MEME output dataset" />
92 <param argument="--meme-full" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-MEME-Full output dataset" />
93 <param argument="--busted" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-BUSTED output dataset" />
94 <param argument="--slac" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-SLAC output dataset" />
95 <param argument="--fel" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-FEL output dataset" />
96 <param argument="--cfel" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-CFEL output dataset" />
97 <param argument="--bgm" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-BGM output dataset" />
98 </when>
99 <when value="merge">
100 <param argument="--summary-inputs" type="data" format="hyphy_results.json" multiple="true" label="Segment annotations to merge" />
101 <param argument="--annotation-inputs" type="data" format="hyphy_results.json" multiple="true" label="Site annotations to merge" />
102 </when>
103 </conditional>
104 </inputs>
105 <outputs>
106 <data name="summary" format="hyphy_results.json" label="${tool.name} on ${on_string} - Segment annotations" />
107 <data name="annotation" format="hyphy_results.json" label="${tool.name} on ${on_string} - Site annotations" />
108 </outputs>
109 <tests>
110 <test>
111 <param name="mode" value="summary" />
112 <param name="name" value="epi_isl_1009769" />
113 <param name="gene" value="nsp8" />
114 <param name="combined" value="summary/nsp8.combined.fas" />
115 <param name="fade" value="summary/nsp8.FADE.json" />
116 <param name="prime" value="summary/nsp8.PRIME.json" />
117 <param name="relax" value="summary/nsp8.RELAX.json" />
118 <param name="meme" value="summary/nsp8.MEME.json" />
119 <param name="meme_full" value="summary/nsp8.MEME-full.json" />
120 <param name="labels" value="summary/nsp8.labels.json" />
121 <param name="busted" value="summary/nsp8.BUSTED.json" />
122 <param name="slac" value="summary/nsp8.SLAC.json" />
123 <param name="fel" value="summary/nsp8.FEL.json" />
124 <param name="cfel" value="summary/nsp8.CFEL.json" />
125 <param name="bgm" value="summary/nsp8.combined.fas.BGM.json" />
126 <output name="summary" file="summary/nsp8-segment.json" />
127 <output name="annotation" file="summary/nsp8-site.json" />
128 </test>
129 <test>
130 <param name="mode" value="summary" />
131 <param name="name" value="epi_isl_1009769" />
132 <param name="gene" value="ORF6" />
133 <param name="combined" value="summary/ORF6.combined.fas" />
134 <param name="fade" value="summary/ORF6.FADE.json" />
135 <param name="meme_full" value="summary/ORF6.MEME-full.json" />
136 <param name="labels" value="summary/ORF6.labels.json" />
137 <param name="slac" value="summary/ORF6.SLAC.json" />
138 <output name="summary" file="summary/ORF6-segment.json" />
139 <output name="annotation" file="summary/ORF6-site.json" />
140 </test>
141 <test>
142 <param name="mode" value="summary" />
143 <param name="name" value="epi_isl_1009769" />
144 <param name="gene" value="nsp7" />
145 <param name="combined" value="summary/nsp7.combined.fas" />
146 <param name="fade" value="summary/nsp7.FADE.json" />
147 <param name="meme_full" value="summary/nsp7.MEME-full.json" />
148 <param name="labels" value="summary/nsp7.labels.json" />
149 <param name="slac" value="summary/nsp7.SLAC.json" />
150 <output name="summary" file="summary/nsp7-segment.json" />
151 <output name="annotation" file="summary/nsp7-site.json" />
152 </test>
153 <test>
154 <param name="mode" value="merge" />
155 <param name="summary_inputs" value="summary/nsp7-segment.json,summary/nsp8-segment.json,summary/ORF6-segment.json" />
156 <param name="annotation_inputs" value="summary/nsp7-site.json,summary/nsp8-site.json,summary/ORF6-site.json" />
157 <output name="summary" file="summary/merged-segment.json" />
158 <output name="annotation" file="summary/merged-site.json" />
159 </test>
160 </tests>
161 <help><![CDATA[
162 HyPhy-Summary
163 =============
164
165 This tool has two operation modes, summary and merge.
166
167 Summary
168 -------
169
170 Given a combined and filtered alignment from TN93-Filter, along with the
171 appropriate HyPhy analysis outputs, this mode will return two JSON files, one
172 with segment annotations and the other with site annotations.
173
174 Analyses required for this mode:
175
176 - FADE
177 - PRIME
178 - RELAX
179 - MEME
180 - MEME-Full
181 - Annotate, with the labels in JSON format
182 - BUSTED
183 - SLAC
184 - FEL
185 - CFEL
186 - BGM
187
188 Merge
189 -----
190
191 This mode takes a set of segment and site annotations, one each per gene that
192 was analyzed, and returns a merged set of site and segment annotations.
193
194 ]]></help>
195 <citations>
196 <citation type="doi">10.1093/bioinformatics/bti079</citation>
197 </citations>
198 </tool>