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"planemo upload for repository https://github.com/Bierinformatik/miRNAture/tree/galaxy_add/Galaxy/miRNAture commit 47a893683a9445abddce77c28f43d098b62cf385"
author cavelandiah
date Sun, 27 Nov 2022 22:00:05 +0000
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1 <tool id="mirnature" name="miRNAture" version="1.1+galaxy0" python_template_version="3.5" 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 ##Last data path from: https://doi.org/10.5281/zenodo.7180160
9 ##MIRNATURE_DATA_PATH=\$(dirname \$(which miRNAture))/../share/blockclust_data &&
10
11 #import re
12 mkdir -p output &&
13 #if $blast_specific.blast_searches == 1:
14 mkdir -p $__tool_directory__/queries_to_test &&
15 cp '$queries_to_blast' $__tool_directory__/queries_to_test/Unknown_specie.fa &&
16 bash $__tool_directory__/generate_blast_folder.sh Unknown_specie.fa > queries_description.txt &&
17 mv queries_description.txt $__tool_directory__/queries_to_test/ &&
18 #end if
19
20 bash $__tool_directory__/create_dataset.sh '$dataset' '$__tool_directory__' &&
21
22 miRNAture
23 -stage '$stage'
24 #if $activate_subset.subset_models_des == 1:
25 -sublist '$subset_models'
26 #end if
27 -nbitscore_cut '$nbitscore'
28 -dataF $__tool_directory__/uncompress/Dataset/
29 -specie_genome '$specie_genome'
30 -specie_name '$specie_name'
31 -specie_tag '$specie_tag'
32 -pe '$parallel_linux_select'
33 -workdir 'output/'
34 -m "${",".join(map(str, $homology_mode)) + ",final"}"
35 #if $blast_specific.blast_searches == 1:
36 #set $joined_str=",".join(map(str, $blast_specific.blast_strategy))
37 #set $complete_str=($joined_str + ",ALL")
38 -strategy '$complete_str'
39 -blastq '$__tool_directory__/queries_to_test/'
40 #end if
41 -rep '$repeat_filter' > '$std_output' &&
42 rm -rf $__tool_directory__/uncompress/
43 ]]></command>
44
45 <inputs>
46 <!--File-->
47 <param argument="-specie_genome" format="fasta" multiple="true" type="data"
48 label="Input genome or sequence"
49 help="Input sequence to be processed by miRNAture" />
50 <!--Hidden-->
51 <param argument="-pe" name="parallel_linux_select" type="integer" value="1" label="Parallel running" help="Test Parallel Linux" >
52 <validator type="in_range" message="Please set this option to 1." min="1" max="1"/>
53 </param>
54
55 <!--TEXT-->
56 <param argument="-specie_name" type="text" label="Scientific specie name as: Genera_specie" />
57 <param argument="-specie_tag" type="text" label="Species tag to identify through experiment" />
58
59 <!--NUM-->
60 <param argument="-nbitscore_cut" name="nbitscore" type="float" label="nBitscore"
61 value="1" min="0" max="1" help="Control bitscore threshold to filter Rfam candidates" />
62
63 <param argument="-rep" name="repeat_filter" type="select" label="Repeats filter" help="Repetition cutoff" >
64 <option value="relax,150,100">relax</option>
65 <option value="default,200,100">default</option>
66 </param>
67
68 <!--Binary-->
69 <conditional name="activate_subset">
70 <!--Binary-->
71 <param argument="-sublist" name="subset_models_des" type="select" label="Subset default miRNA families" help="Make a selection of specific miRNA families to be search">
72 <option value="0">No</option>
73 <option value="1">Yes</option>
74 </param>
75 <when value="0">
76 </when>
77 <when value="1">
78 <param format="txt" multiple="true" name="subset_models" type="data"
79 label="List of miRNA models to be searched"
80 help="Input sequence to be processed by miRNAture" optional="true"/>
81 </when>
82 </conditional>
83
84 <param argument="-dataF" format="gz" multiple="true" name="dataset" type="data"
85 label="Input Pre-calculated data"
86 help="Please submit the pre-calculated data to run miRNAture (see https://doi.org/10.5281/zenodo.7180160)" />
87
88 <!--Static list-->
89 <param argument="-stage" type="select" label="Stages to run">
90 <option value="complete">complete</option>
91 <option value="homology">homology</option>
92 <option value="no_homology">no_homology</option>
93 <option value="validation">validation</option>
94 <option value="evaluation">evaluation</option>
95 <option value="summarise">summarise</option>
96 </param>
97 <!--Check Boxes-->
98 <param argument="-mode" name="homology_mode" type="select" multiple="true" label="Homology mode">
99 <option value="blast">blast</option>
100 <option value="rfam">rfam</option>
101 <option value="mirbase">mirbase</option>
102 <option value="hmm">hmm</option>
103 </param>
104
105 <conditional name="blast_specific">
106 <param name="blast_searches" type="select" label="Use the blast mode to search annotated queries in your target genome?" help="Activate this option if wanted to use blast mode with provided sequences">
107 <option value="0">No</option>
108 <option value="1">Yes</option>
109 </param>
110 <when value="0">
111 </when>
112 <when value="1">
113 <param argument="-strategy" name="blast_strategy" type="select" multiple="true" label="Select one or more blast strategy(ies)">
114 <option value="1">1</option>
115 <option value="2">2</option>
116 <option value="3">3</option>
117 <option value="4">4</option>
118 <option value="5">5</option>
119 <option value="6">6</option>
120 <option value="7">7</option>
121 <option value="8">8</option>
122 <option value="9">9</option>
123 </param>
124 <param argument="-blstq" format="fasta" multiple="true" name="queries_to_blast" type="data"
125 label="Query sequences"
126 help="Query sequences to search in target genome" />
127 </when>
128 </conditional>
129 </inputs>
130
131 <outputs>
132 <data name="std_output" format="txt" label="Standard output miRNAture" />
133 <data format="txt" name="report0" label="Homology output miRNAture">
134 <filter>stage == "homology" </filter>
135 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.yaml" directory="output/" ext="yaml" visible="true"/>
136 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gff3" directory="output/miRNA_prediction/Final_Candidates" ext="gff3" visible="true" />
137 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt\.db" directory="output/miRNA_prediction/Final_Candidates" visible="true" />
138 </data>
139 <data format="txt" name="report1" label="Complete output miRNAture">
140 <filter>stage == "complete" </filter>
141 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.yaml" directory="output/" ext="yaml" visible="true"/>
142 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gff3" directory="output/Final_miRNA_evaluation" ext="gff3" visible="true" />
143 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="output/Final_miRNA_evaluation" ext="txt" visible="true" />
144 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta" directory="output/Final_miRNA_evaluation/Fasta" ext="fasta" visible="true" />
145 </data>
146 </outputs>
147 <tests>
148 <test>
149 <param name="stage" value="homology"/>
150 <conditional name="activate_subset">
151 <param name="subset_models_des" value="1"/>
152 <param name="subset_models" value="fam.txt"/>
153 </conditional>
154 <param name="nbitscore" value="1.0"/>
155 <param name="dataset" value="Dataset_mirnature_tutorial.tar.gz"/>
156 <param name="specie_genome" value="test.fasta"/>
157 <param name="specie_name" value="Test_specie"/>
158 <param name="specie_tag" value="Test"/>
159 <param name="homology_mode" value="hmm"/>
160 <param name="parallel_linux_select" value="1"/>
161 <param name="repeat_filter" value="relax"/>
162 <output name="std_output" file="test.txt"/>
163 </test>
164 </tests>
165
166 <help><![CDATA[
167
168 **miRNAture** detects *bona fide* miRNA candidates through sequence homology
169 searches and validation steps using structural alignments with
170 pre-defined or/and modified miRNA-specific covariance models. The
171 miRNAture pipeline is composed of three modules: (1) Homology search
172 operating on miRNA precursors, (2) prediction of the positioning of
173 mature miRNAs within the precursor mature annotation, and (3) an
174 Evaluation scheme designed to identify false positive miRNA annotations.
175 This multi-stage approach generates annotation files in BED/GFF3 from
176 precursors and detected mature regions and corresponding FASTA files. At
177 the same time, a summary file with the MFE, precursor length and number
178 of loci of each annotated miRNA family.
179
180 AUTHORS:
181 *Cristian A. Velandia Huerto*, *Joerg Fallmann* and *Peter F. Stadler*
182
183 USAGE:
184 ./miRNAture [-options]
185
186 OPTIONS:
187 -h/-help Print this documentation.
188
189 -blstq/-blastQueriesFolder <PATH>
190 Path of blast query sequences in FASTA format to be searched
191 on the subject sequence.
192
193 -dataF/-datadir <PATH>
194 Path to pre-calculated data directory containing RFAM and
195 miRBase covariance, hidden markov models, and necessary
196 files to run MIRfix.
197
198 -m/-mode <blast,hmm,rfam,mirbase>
199 Homology search modes: blast, hmm, rfam, mirbase, and/or infernal.
200 It is possible to perform individual analysis, but in this Galaxy
201 version is always included the *final* option to merge multiple results.
202
203 -rep/-repetition_cutoff <relax,Number_Loci,Candidates_to_evaluate>
204 Setup number of maximum loci number that will be evaluated
205 by the mature's annotation stage. By default, miRNAture will
206 detect miRNA families that report high number of loci (> 200
207 loci). Then, it will select the top 100 candidates in terms
208 of alignment scores, as candidates for the validation stage
209 (default,200,100). The designed values could be modified by
210 the following flag in the command line version:
211 'relax,Number_Loci,Candidates_to_evaluate'. This option
212 allows to the user to select the threshold values to detect
213 repetitive families. The first parameter is <relax>, which
214 tells miRNAture to change the default configuration. The
215 next one, <Number_Loci> is the threshold of loci number to
216 classify a family as repetitive. The last one,
217 <Candidates_to_evaluate>, is the number of candidates prone
218 to be evaluated in the next evaluation section. The rest
219 candidates are included as homology 'potential' candidates.
220 Selected option for this Galaxy version is set as:
221 <relax,150,100>.
222
223 -str/-strategy <1,2,3,4,5,6,7,8,9,10>
224 This flag is blast mode specific. It corresponds to blast
225 strategies that would be used to search miRNAs. It must be
226 indicated along with -m *Blast* flag.
227
228 -stg/-stage <'homology','no_homology','validation','evaluation','summarise','complete'>
229 Selects the stage to be run on miRNAture. The options are:
230 'homology', 'no_homology', 'validation', 'evaluation',
231 'summarise' or 'complete'.
232
233 -speG/-specie_genome <PATH>
234 Path of target sequences to be analyzed in FASTA format.
235
236 -speN/-specie_name <Genera_specie>
237 Specie or sequence source's scientific name. The format must
238 be: *Genera_specie*, separated by '_'.
239
240 -speT/-specie_tag <TAG_NAME>
241 Experiment tag. Will help to identify the generated files
242 along miRNA output files.
243
244 -sublist/-subset_models <FILE_WITH_CM_NAMES>
245 Target list of CMs to be searched on subject
246 genome/sequences. If not indicated, miRNAture will run all
247 RFAM v14.4 metazoan miRNA models.
248
249 -w/-workdir <OUT_PATH>
250 Working directory path to write all miRNAture results.
251
252 BUGS, CAVEATS, COMPLAINS or DONATIONS
253 Write directly to cristian at bioinf.uni-leipzig.de
254
255 ]]></help>
256 <expand macro="citations" />
257 </tool>