Mercurial > repos > iuc > mirnature
comparison mirnature.xml @ 0:dd2f87ccbd2c draft default tip
planemo upload for repository https://github.com/Bierinformatik/miRNAture commit 9e4e624a3a486cbd805bc3beb00e9903f315efe0
author | iuc |
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date | Sun, 11 Dec 2022 22:28:10 +0000 |
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-1:000000000000 | 0:dd2f87ccbd2c |
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1 <tool id="mirnature" name="miRNAture" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |
2 <description>Computational detection of canonical microRNAs</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="aggressive"><![CDATA[ | |
8 #import re | |
9 mkdir -p uncompress && | |
10 mkdir -p queries_to_test && | |
11 mkdir -p temporal && | |
12 mkdir -p output && | |
13 | |
14 cp '$speG' temporal/genome.fasta && | |
15 #if $blast_strategy: | |
16 cp '$queries_to_blast' queries_to_test/Unknown_species.fa && | |
17 echo "Unknown_species.fa miRNA Unknown species" > queries_to_test/queries_description.txt && | |
18 #end if | |
19 | |
20 #if str('$database_source.database_source_selector') == "cached": | |
21 ln -s '$dataset.fields.path' uncompress/data.gz && | |
22 #else: | |
23 ln -s '$dataset' uncompress/data.gz && | |
24 #end if | |
25 tar -xf uncompress/data.gz --directory uncompress/ && | |
26 rm uncompress/data.gz && | |
27 ## Change name of user folder to Dataset | |
28 mv uncompress/* uncompress/Dataset && | |
29 | |
30 miRNAture | |
31 -stage '$stage' | |
32 #if $subset_models | |
33 -sublist '$subset_models' | |
34 #end if | |
35 -nbitscore_cut '$nbitscore' | |
36 -dataF 'uncompress/Dataset/' | |
37 -speG 'temporal/genome.fasta' | |
38 -speN '$speN' | |
39 -speT '$speT' | |
40 -pe '1' | |
41 -workdir 'output/' | |
42 -m "${",".join(map(str, $homology_mode)) + ",final"}" | |
43 #if $blast_strategy: | |
44 -strategy "${",".join(map(str, $blast_strategy)) + ",ALL"}" | |
45 -blstq 'queries_to_test/' | |
46 #end if | |
47 -rep '$repeat_filter' > '$std_output' | |
48 ]]></command> | |
49 | |
50 <inputs> | |
51 <!--File--> | |
52 <param argument="-speG" format="fasta" multiple="true" type="data" | |
53 label="Input genome or sequence" | |
54 help="Input sequence to be processed by miRNAture" /> | |
55 | |
56 <!--TEXT--> | |
57 <param argument="-speN" type="text" label="Scientific species name written separated by '_', such as: Homo_sapiens" > | |
58 <validator type="regex" message="Only letters and underscores are allowed">^[\(\w\)]+$</validator> | |
59 </param> | |
60 <param argument="-speT" type="text" label="Species tag to identify through experiment (i.e short 4 letters tag)" > | |
61 <validator type="regex" message="Please write only letters">^[a-zA-Z]+$</validator> | |
62 </param> | |
63 | |
64 <!--NUM--> | |
65 <param argument="-nbitscore_cut" name="nbitscore" type="float" label="nBitscore" | |
66 value="1" min="0" max="1" help="Control of normalized bitscore (nbitscore) threshold to filter Rfam candidates" /> | |
67 | |
68 <param argument="-rep" name="repeat_filter" type="select" label="Repeats filter" help="Repetition cutoff" > | |
69 <option value="relax,150,100">relax</option> | |
70 <option value="default,200,100">default</option> | |
71 </param> | |
72 | |
73 <param format="txt" multiple="true" name="subset_models" type="data" | |
74 label="List of miRNA models to be searched" | |
75 help="Input sequence to be processed by miRNAture" optional="true"/> | |
76 | |
77 <conditional name="database_source"> | |
78 <param argument="-dataF" name="database_source_selector" type="select" label="Choose the source for the database"> | |
79 <option value="cached">Pre-defined datasets</option> | |
80 <option value="history">History</option> | |
81 </param> | |
82 <when value="cached"> | |
83 <param name="dataset" type="select" help="Select a pre-calculated dataset to run miRNAture (i.e. https://doi.org/10.5281/zenodo.7180160)" label="Pre-calculated datasets" > | |
84 <options from_data_table="mirnature_selection" /> | |
85 <validator message="No reference dataset is available for miRNAture" type="no_options" /> | |
86 </param> | |
87 </when> | |
88 <when value="history"> | |
89 <param name="dataset" format="gz" type="data" label="Input user Pre-calculated dataset" help="Please submit the pre-calculated data to run miRNAture (i.e https://doi.org/10.5281/zenodo.7180160)" /> | |
90 </when> | |
91 </conditional> | |
92 | |
93 <!--Static list--> | |
94 <param argument="-stage" type="select" label="Select one miRNAture stage"> | |
95 <option value="complete">complete</option> | |
96 <option value="homology">homology</option> | |
97 </param> | |
98 <!--Check Boxes--> | |
99 <param argument="-mode" name="homology_mode" type="select" multiple="true" label="Homology mode"> | |
100 <option value="blast">blast</option> | |
101 <option value="rfam">rfam</option> | |
102 <option value="mirbase">mirbase</option> | |
103 <option value="hmm">hmm</option> | |
104 </param> | |
105 <param argument="-strategy" name="blast_strategy" optional="true" type="select" multiple="true" | |
106 label="Select one or more pre-calculated set of blastn parameters, accordingly to the miRNAture publication."> | |
107 <option value="1">1</option> | |
108 <option value="2">2</option> | |
109 <option value="3">3</option> | |
110 <option value="4">4</option> | |
111 <option value="5">5</option> | |
112 <option value="6">6</option> | |
113 <option value="7">7</option> | |
114 <option value="8">8</option> | |
115 <option value="9">9</option> | |
116 </param> | |
117 <param argument="-blstq" format="fasta" multiple="true" name="queries_to_blast" type="data" label="Query sequences" | |
118 help="Query sequences to search in target genome" optional="true" /> | |
119 </inputs> | |
120 | |
121 <outputs> | |
122 <data name="std_output" format="txt" label="Standard output miRNAture" /> | |
123 <collection name="gff3_files_h" type="list" label="${tool.name} on ${on_string}: GFF3 file"> | |
124 <discover_datasets pattern="(?P<designation>.+)\.gff3" directory="output/miRNA_prediction/Final_Candidates/" format="gff3" visible="true" /> | |
125 <filter> stage == "homology" </filter> | |
126 </collection> | |
127 <collection name="tab_files_h" type="list" label="${tool.name} on ${on_string}: Additional Files"> | |
128 <discover_datasets pattern="(?P<designation>.+)\-potential\.txt" directory="output/miRNA_prediction/Final_Candidates/" format="txt" visible="true" /> | |
129 <filter> stage == "homology" </filter> | |
130 </collection> | |
131 <collection name="yaml_files_h" type="list" label="${tool.name} on ${on_string}: YAML file"> | |
132 <discover_datasets pattern="(?P<designation>.+)\.yaml" directory="output" format="yaml" visible="true"/> | |
133 <filter> stage == "homology" </filter> | |
134 </collection> | |
135 <collection name="gff3_files_c" type="list" label="${tool.name} on ${on_string}: GFF3 file"> | |
136 <discover_datasets pattern="(?P<designation>.+)\.gff3" directory="output/miRNA_prediction/Final_Candidates/" format="gff3" visible="true" /> | |
137 <discover_datasets pattern="(?P<designation>.+)\.gff3" directory="output/Final_miRNA_evaluation/" ext="gff3" format="gff3" visible="true" /> | |
138 <filter> stage == "complete" </filter> | |
139 </collection> | |
140 <collection name="bed_files_c" type="list" label="${tool.name} on ${on_string}: BED file"> | |
141 <discover_datasets pattern="(?P<designation>.+)\.bed" directory="output/Final_miRNA_evaluation/" ext="bed" format="bed" visible="true" /> | |
142 <filter> stage == "complete" </filter> | |
143 </collection> | |
144 <collection name="fasta_files_c" type="list" label="${tool.name} on ${on_string}: Fasta files"> | |
145 <discover_datasets pattern="(?P<designation>.+)\.fasta" directory="output/Final_miRNA_evaluation/Fasta" ext="fasta" format="fasta" visible="true" /> | |
146 <filter> stage == "complete" </filter> | |
147 </collection> | |
148 <collection name="statistics_files_c" type="list" label="${tool.name} on ${on_string}: Summary file"> | |
149 <discover_datasets pattern="(?P<designation>.+)\.txt" directory="output/Final_miRNA_evaluation/" ext="txt" format="txt" visible="true" /> | |
150 <filter> stage == "complete" </filter> | |
151 </collection> | |
152 <collection name="yaml_files_c" type="list" label="${tool.name} on ${on_string}: YAML file"> | |
153 <discover_datasets pattern="(?P<designation>.+)\.yaml" directory="output" ext="yaml" format="yaml" visible="true"/> | |
154 <filter> stage == "complete" </filter> | |
155 </collection> | |
156 </outputs> | |
157 | |
158 <tests> | |
159 <!-- HMM Rfam search --> | |
160 <test expect_exit_code="0"> | |
161 <param name="stage" value="homology"/> | |
162 <param name="subset_models" value="fam.txt"/> | |
163 <param name="nbitscore" value="1.0"/> | |
164 <param name="database_source_selector" value="history" /> | |
165 <param name="dataset" value="Dataset_mirnature_tutorial.tar.gz"/> | |
166 <param name="speG" value="genome.fasta"/> | |
167 <param name="speN" value="Unknown_species"/> | |
168 <param name="speT" value="Unsg"/> | |
169 <param name="homology_mode" value="hmm"/> | |
170 <param name="repeat_filter" value="relax"/> | |
171 <output name="std_output" file="test_hmm.txt" ftype="txt"/> | |
172 <output_collection name="gff3_files_h" count="1"/> | |
173 <output_collection name="yaml_files_h" count="1"/> | |
174 <output_collection name="tab_files_h" count="1"/> | |
175 </test> | |
176 <!-- Infernal Rfam search --> | |
177 <test expect_exit_code="0"> | |
178 <param name="stage" value="homology"/> | |
179 <param name="subset_models" value="fam.txt"/> | |
180 <param name="nbitscore" value="1.0"/> | |
181 <param name="database_source_selector" value="history" /> | |
182 <param name="dataset" value="Dataset_mirnature_tutorial.tar.gz"/> | |
183 <param name="speG" value="genome.fasta"/> | |
184 <param name="speN" value="Unknown_species"/> | |
185 <param name="speT" value="Unsp"/> | |
186 <param name="homology_mode" value="rfam"/> | |
187 <param name="repeat_filter" value="relax"/> | |
188 <output name="std_output" file="test_rfam.txt" ftype="txt"/> | |
189 <output_collection name="gff3_files_h" count="1"/> | |
190 <output_collection name="yaml_files_h" count="1"/> | |
191 <output_collection name="tab_files_h" count="1"/> | |
192 </test> | |
193 <!-- Infernal miRBase search --> | |
194 <test expect_exit_code="0"> | |
195 <param name="stage" value="homology"/> | |
196 <param name="subset_models" value="fam.txt"/> | |
197 <param name="nbitscore" value="1.0"/> | |
198 <param name="database_source_selector" value="history" /> | |
199 <param name="dataset" value="Dataset_mirnature_tutorial.tar.gz"/> | |
200 <param name="speG" value="genome.fasta"/> | |
201 <param name="speN" value="Unknown_species"/> | |
202 <param name="speT" value="Unsd"/> | |
203 <param name="homology_mode" value="mirbase"/> | |
204 <param name="repeat_filter" value="relax"/> | |
205 <output name="std_output" file="test_mirbase.txt" ftype="txt"/> | |
206 <output_collection name="gff3_files_h" count="1"/> | |
207 <output_collection name="yaml_files_h" count="1"/> | |
208 <output_collection name="tab_files_h" count="1"/> | |
209 </test> | |
210 <!-- Combined all homology search --> | |
211 <test expect_exit_code="0"> | |
212 <param name="stage" value="homology"/> | |
213 <param name="subset_models" value="fam.txt"/> | |
214 <param name="nbitscore" value="1.0"/> | |
215 <param name="database_source_selector" value="history" /> | |
216 <param name="dataset" value="Dataset_mirnature_tutorial.tar.gz"/> | |
217 <param name="speG" value="genome.fasta"/> | |
218 <param name="speN" value="Unknown_species"/> | |
219 <param name="speT" value="Unsp"/> | |
220 <param name="homology_mode" value="blast,hmm,rfam,mirbase"/> | |
221 <param name="blast_strategy" value="8,9"/> | |
222 <param name="queries_to_blast" value="test.fasta"/> | |
223 <param name="repeat_filter" value="relax"/> | |
224 <output name="std_output" file="test_all_homology.txt" ftype="txt"/> | |
225 <output_collection name="gff3_files_h" count="1"/> | |
226 <output_collection name="yaml_files_h" count="1"/> | |
227 <output_collection name="tab_files_h" count="1"/> | |
228 </test> | |
229 </tests> | |
230 | |
231 <help><![CDATA[ | |
232 | |
233 **miRNAture** detects *bona fide* miRNA candidates through sequence homology searches and validation steps using structural alignments | |
234 with pre-defined or/and modified miRNA-specific covariance models. The miRNAture pipeline is composed of three modules: | |
235 | |
236 #. Homology search operating on miRNA precursors | |
237 #. Prediction of the positioning of mature miRNAs within the precursor mature annotation | |
238 #. Evaluation scheme designed to identify false positive miRNA annotations. | |
239 | |
240 This multi-stage approach generates annotation files in BED/GFF3 from precursors and detected mature regions and corresponding FASTA files. | |
241 At the same time, a summary file with the MFE, precursor length and number of loci of each annotated miRNA family. | |
242 | |
243 ]]></help> | |
244 <expand macro="creators" /> | |
245 <expand macro="citations" /> | |
246 </tool> |