Mercurial > repos > iuc > semibin_generate_sequence_features

comparison macros.xml @ 2:f5aff7c9a65d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
author iuc
date Tue, 25 Mar 2025 15:49:59 +0000
parents cae8e4d4f726
children b55f0ce54d97
comparison
equal deleted inserted replaced
1:cae8e4d4f726 2:f5aff7c9a65d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.5.1</token> 3 <token name="@TOOL_VERSION@">2.0.2</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">1</token>
5 <token name="@PROFILE@">21.01</token> 5 <token name="@PROFILE@">21.01</token>
6 <xml name="biotools"> 6 <xml name="biotools">
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">semibin</xref> 8 <xref type="bio.tools">semibin</xref>
9 </xrefs> 9 </xrefs>
13 <requirement type="package" version="@TOOL_VERSION@">semibin</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">semibin</requirement>
14 <yield/> 14 <yield/>
15 </requirements> 15 </requirements>
16 </xml> 16 </xml>
17 <xml name="version"> 17 <xml name="version">
18 <version_command>SemiBin -v</version_command> 18 <version_command>SemiBin2 -v</version_command>
19 </xml> 19 </xml>
20 <xml name="mode_fasta_bam"> 20 <xml name="mode_fasta_bam">
21 <conditional name="mode"> 21 <conditional name="mode">
22 <expand macro="mode_select"/> 22 <expand macro="mode_select"/>
23 <when value="single"> 23 <when value="single">
107 #else 107 #else
108 ln -s '$e' '${identifier}.fasta' && 108 ln -s '$e' '${identifier}.fasta' &&
109 #end if 109 #end if
110 #end for 110 #end for
111 #set $separator = ':' 111 #set $separator = ':'
112 SemiBin concatenate_fasta 112 SemiBin2 concatenate_fasta
113 --input-fasta *.fasta 113 --input-fasta *.fasta
114 --output 'output' 114 --output 'output'
115 --separator '$separator' 115 --separator '$separator'
116 --compression none
116 -m $mode.multi_fasta.min_len 117 -m $mode.multi_fasta.min_len
117 && 118 &&
118 ln -s 'output/concatenated.fa' 'contigs.fasta' && 119 ln -s 'output/concatenated.fa' 'contigs.fasta' &&
119 #end if 120 #end if
120 #end if 121 #end if
137 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) 138 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
138 ln -s '$e' '${identifier}.bam' && 139 ln -s '$e' '${identifier}.bam' &&
139 #end for 140 #end for
140 #end if 141 #end if
141 ]]></token> 142 ]]></token>
143 <xml name="ref_select_cannot">
144 <param name="select" type="select" label="Reference database">
145 <option value="cached">Cached database</option>
146 <option value="taxonomy">Pre-computed taxonomy</option>
147 </param>
148 </xml>
142 <xml name="ref_select"> 149 <xml name="ref_select">
143 <param name="select" type="select" label="Reference database"> 150 <param name="select" type="select" label="Reference database">
144 <option value="cached" selected="true">Cached database</option> 151 <option value="ml" selected="true">Use SemiBin ML function</option>
152 <option value="cached">Cached database</option>
145 <option value="taxonomy">Pre-computed taxonomy</option> 153 <option value="taxonomy">Pre-computed taxonomy</option>
146 </param> 154 </param>
147 </xml> 155 </xml>
148 <xml name="cached_db"> 156 <xml name="cached_db">
149 <param name="cached_db" label="Cached databases" type="select"> 157 <param name="cached_db" label="Cached databases" type="select">
150 <options from_data_table="gtdb"> 158 <options from_data_table="gtdb">
151 <validator message="No GTDB database is available" type="no_options" /> 159 <validator message="No GTDB database is available" type="no_options" />
152 </options> 160 </options>
153 </param> 161 </param>
154 </xml> 162 </xml>
163 <xml name="ref-single-cannot">
164 <conditional name="ref">
165 <expand macro="ref_select_cannot"/>
166 <when value="cached">
167 <expand macro="cached_db"/>
168 </when>
169 <when value="taxonomy">
170 <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
171 </when>
172 </conditional>
173 </xml>
174 <xml name="ref-multi-cannot">
175 <conditional name="ref">
176 <expand macro="ref_select_cannot"/>
177 <when value="cached">
178 <expand macro="cached_db"/>
179 </when>
180 <when value="taxonomy">
181 <param argument="--taxonomy-annotation-table" type="data" format="tabular" multiple="true" label="Pre-computed mmseqs2 format taxonomy TSV file" help="One per bin file"/>
182 </when>
183 </conditional>
184 </xml>
155 <xml name="ref-single"> 185 <xml name="ref-single">
156 <conditional name="ref"> 186 <conditional name="ref">
157 <expand macro="ref_select"/> 187 <expand macro="ref_select"/>
158 <when value="cached"> 188 <when value="cached">
159 <expand macro="cached_db"/> 189 <expand macro="cached_db"/>
160 </when> 190 </when>
161 <when value="taxonomy"> 191 <when value="taxonomy">
162 <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/> 192 <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
163 </when> 193 </when>
194 <when value="ml"/>
164 </conditional> 195 </conditional>
165 </xml> 196 </xml>
166 <xml name="ref-multi"> 197 <xml name="ref-multi">
167 <conditional name="ref"> 198 <conditional name="ref">
168 <expand macro="ref_select"/> 199 <expand macro="ref_select"/>
170 <expand macro="cached_db"/> 201 <expand macro="cached_db"/>
171 </when> 202 </when>
172 <when value="taxonomy"> 203 <when value="taxonomy">
173 <param argument="--taxonomy-annotation-table" type="data" format="tabular" multiple="true" label="Pre-computed mmseqs2 format taxonomy TSV file" help="One per bin file"/> 204 <param argument="--taxonomy-annotation-table" type="data" format="tabular" multiple="true" label="Pre-computed mmseqs2 format taxonomy TSV file" help="One per bin file"/>
174 </when> 205 </when>
206 <when value="ml"/>
175 </conditional> 207 </conditional>
176 </xml> 208 </xml>
177 <xml name="ref_single"> 209 <xml name="ref_single">
178 <conditional name="ref"> 210 <conditional name="ref">
179 <expand macro="ref_select"/> 211 <expand macro="ref_select"/>
181 <expand macro="cached_db"/> 213 <expand macro="cached_db"/>
182 </when> 214 </when>
183 <when value="taxonomy"> 215 <when value="taxonomy">
184 <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/> 216 <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
185 </when> 217 </when>
218 <when value="ml"/>
186 </conditional> 219 </conditional>
187 </xml> 220 </xml>
188 <xml name="min_len"> 221 <xml name="min_len">
189 <conditional name="min_len"> 222 <conditional name="min_len">
190 <param name="method" type="select" label="Method to set up the minimal length for contigs in binning"> 223 <param name="method" type="select" label="Method to set up the minimal length for contigs in binning">
220 <xml name="batch-size"> 253 <xml name="batch-size">
221 <param argument="--batch-size" type="integer" min="0" value="2048" label="Batch size used in the training process"/> 254 <param argument="--batch-size" type="integer" min="0" value="2048" label="Batch size used in the training process"/>
222 </xml> 255 </xml>
223 <xml name="orf-finder"> 256 <xml name="orf-finder">
224 <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins"> 257 <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins">
225 <option value="prodigal" selected="true">Prodigal</option> 258 <option value="fast-naive" selected="true">Fast-Naive</option>
259 <option value="prodigal">Prodigal</option>
226 <option value="fraggenescan">Fraggenescan</option> 260 <option value="fraggenescan">Fraggenescan</option>
227 </param> 261 </param>
228 </xml> 262 </xml>
229 <xml name="max-node"> 263 <xml name="max-node">
230 <param argument="--max-node" type="float" min="0" max="1" value="1" label="Fraction of contigs that considered to be binned"/> 264 <param argument="--max-node" type="float" min="0" max="1" value="1" label="Fraction of contigs that considered to be binned"/>
249 </param> 283 </param>
250 </xml> 284 </xml>
251 <xml name="minfasta-kbs"> 285 <xml name="minfasta-kbs">
252 <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/> 286 <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/>
253 </xml> 287 </xml>
254 <xml name="no-recluster"> 288 <xml name="write_pre_reclustering_bins">
255 <param argument="--no-recluster" type="boolean" truevalue="--no-recluster" falsevalue="" checked="false" label="Do not recluster bins?"/> 289 <param argument="--write-pre-reclustering-bins" type="boolean" truevalue="--write-pre-reclustering-bins" falsevalue="" checked="false" label="Return also the pre reclustered bins?"/>
256 </xml> 290 </xml>
257 <xml name="data"> 291 <xml name="data">
258 <param argument="--data" type="data" format="csv" label="Train data"/> 292 <param argument="--data" type="data" format="csv" label="Train data"/>
259 </xml> 293 </xml>
260 <xml name="data_output_single"> 294 <xml name="data_output_single">
308 </collection> 342 </collection>
309 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs"> 343 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
310 <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter> 344 <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter>
311 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" /> 345 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
312 </collection> 346 </collection>
347
313 </xml> 348 </xml>
314 <xml name="train_output"> 349 <xml name="train_output">
315 <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" /> 350 <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />
316 </xml> 351 </xml>
317 <xml name="cannot_link_output"> 352 <xml name="cannot_link_output">