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comparison mafft.xml @ 16:8e649f27aa0d draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 3d98df472498e1273369d23822d10db14f337443
author bgruening
date Thu, 22 Aug 2024 19:20:24 +0000
parents bf28a8cff401
children
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15:bf28a8cff401 16:8e649f27aa0d
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="biotools"/> 7 <expand macro="biotools"/>
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 <stdio> 9 <version_command>mafft --version</version_command>
10 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> 10 <command detect_errors="exit_code"><![CDATA[
11 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
12 </stdio>
13 <version_command><![CDATA[mafft --version]]></version_command>
14 <command><![CDATA[
15 ## Concatenate all input datasets no matter how they were provided 11 ## Concatenate all input datasets no matter how they were provided
16 bash inputs.sh && 12 bash inputs.sh &&
17 13
18 ## Count total number of sequences across input datasets 14 ## Count total number of sequences across input datasets
19 ## Can't do this on the concatenated input data prepared above because it's 15 ## Can't do this on the concatenated input data prepared above because it's
168 <param name="inputs" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format. Add Dataset for concatenation of every additional dataset with each file of the first upload panel"/> 164 <param name="inputs" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format. Add Dataset for concatenation of every additional dataset with each file of the first upload panel"/>
169 </repeat> 165 </repeat>
170 </when> 166 </when>
171 <when value="merge"> 167 <when value="merge">
172 <repeat name="batches" title="Input batch" default="1" min="1"> 168 <repeat name="batches" title="Input batch" default="1" min="1">
173 <param name="inputs" multiple="true" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/> 169 <param name="inputs" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format." multiple="true"/>
174 </repeat> 170 </repeat>
175 </when> 171 </when>
176 </conditional> 172 </conditional>
177 <conditional name="datatype_selection"> 173 <conditional name="datatype_selection">
178 <param name="datatype" type="select" label="Type of sequences" help="The tool can try to detect the type of the input sequences, but you likely want to declare it explicitly. Doing so will also give you control over the scoring matrix used for the alignment, while autodetection will result in the Kimura PAM200 and the BLOSUM62 matrix being used for nucleic acids and protein alignments, respectively."> 174 <param name="datatype" type="select" label="Type of sequences" help="The tool can try to detect the type of the input sequences, but you likely want to declare it explicitly. Doing so will also give you control over the scoring matrix used for the alignment, while autodetection will result in the Kimura PAM200 and the BLOSUM62 matrix being used for nucleic acids and protein alignments, respectively.">
185 <conditional name="scoring_matrix"> 181 <conditional name="scoring_matrix">
186 <param name="type" type="select" label="Type of scoring matrix" help="See the tool help below for details about the available options."> 182 <param name="type" type="select" label="Type of scoring matrix" help="See the tool help below for details about the available options.">
187 <option value="--kimura">Kimura</option> 183 <option value="--kimura">Kimura</option>
188 </param> 184 </param>
189 <when value="--kimura"> 185 <when value="--kimura">
190 <param argument="--kimura" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix" /> 186 <param name="coefficient" argument="--kimura" type="integer" min="1" value="200" label="PAM value of the matrix" />
191 </when> 187 </when>
192 </conditional> 188 </conditional>
193 <expand macro="misc_scoring_scheme" /> 189 <expand macro="misc_scoring_scheme" />
194 </when> 190 </when>
195 <when value="--amino"> 191 <when value="--amino">
199 <option value="--jtt">JTT</option> 195 <option value="--jtt">JTT</option>
200 <option value="--tm">transmembrane protein-optimized JTT</option> 196 <option value="--tm">transmembrane protein-optimized JTT</option>
201 <option value="custom">custom matrix</option> 197 <option value="custom">custom matrix</option>
202 </param> 198 </param>
203 <when value="--bl"> 199 <when value="--bl">
204 <param argument="--bl" name="coefficient" type="select" display="radio" label="Coefficient of the BLOSUM matrix"> 200 <param name="coefficient" argument="--bl" type="select" label="Coefficient of the BLOSUM matrix" display="radio">
205 <option value="30">30</option> 201 <option value="30">30</option>
206 <option value="45">45</option> 202 <option value="45">45</option>
207 <option value="62" selected="true">62</option> 203 <option value="62" selected="true">62</option>
208 <option value="80">80</option> 204 <option value="80">80</option>
209 </param> 205 </param>
210 </when> 206 </when>
211 <when value="--jtt"> 207 <when value="--jtt">
212 <param argument="--jtt" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix" /> 208 <param name="coefficient" argument="--jtt" type="integer" min="1" value="200" label="PAM value of the matrix" />
213 </when> 209 </when>
214 <when value="--tm"> 210 <when value="--tm">
215 <param argument="--tm" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix"/> 211 <param name="coefficient" argument="--tm" type="integer" min="1" value="200" label="PAM value of the matrix"/>
216 </when> 212 </when>
217 <when value="custom"> 213 <when value="custom">
218 <param argument="--aamatrix" type="data" format="txt" label="User-defined AA scoring matrix" help="The expected format of the matrix is the same as that used by BLAST."/> 214 <param argument="--aamatrix" type="data" format="txt" label="User-defined AA scoring matrix" help="The expected format of the matrix is the same as that used by BLAST."/>
219 </when> 215 </when>
220 </conditional> 216 </conditional>
265 <option value="--localpair">Local alignment (Smith-Waterman) (--localpair)</option> 261 <option value="--localpair">Local alignment (Smith-Waterman) (--localpair)</option>
266 <option value="--genafpair">Local, affine gap cost (--genafpair)</option> 262 <option value="--genafpair">Local, affine gap cost (--genafpair)</option>
267 <option value="--fastapair">All pairwise alignments are computed with FASTA (--fastapair)</option> 263 <option value="--fastapair">All pairwise alignments are computed with FASTA (--fastapair)</option>
268 </param> 264 </param>
269 <when value="--6merpair"> 265 <when value="--6merpair">
270 <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is build this number of times in the progressive stage."/> 266 <param argument="--retree" type="integer" min="1" max="3" value="2" label="Guide tree is build this number of times in the progressive stage."/>
271 </when> 267 </when>
272 <when value="--globalpair"> 268 <when value="--globalpair">
273 <expand macro="global_align_options"/> 269 <expand macro="global_align_options"/>
274 <expand macro="weighti_param" /> 270 <expand macro="weighti_param" />
275 </when> 271 </when>
310 </when> 306 </when>
311 </conditional> 307 </conditional>
312 </when> 308 </when>
313 </conditional> 309 </conditional>
314 <section name="progressive_alignment_calculation" title="Progressive alignment calculation" expanded="true"> 310 <section name="progressive_alignment_calculation" title="Progressive alignment calculation" expanded="true">
315 <param argument="--maxiterate" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" /> 311 <param argument="--maxiterate" type="integer" min="0" max="1000" value="0" label="Maximum number of iterations" help="1000 for maximum quality" />
316 <param argument="--fft" type="boolean" truevalue="--fft" falsevalue="--nofft" checked="True" label="Use FFT approximation in group-to-group alignment?" /> 312 <param argument="--fft" type="boolean" truevalue="--fft" falsevalue="--nofft" checked="True" label="Use FFT approximation in group-to-group alignment?" />
317 <param argument="--noscore" type="boolean" truevalue="" falsevalue="--noscore" checked="True" label="Check alignment score in the iterative refinement stage?" /> 313 <param argument="--noscore" type="boolean" truevalue="" falsevalue="--noscore" checked="True" label="Check alignment score in the iterative refinement stage?" />
318 </section> 314 </section>
319 </when> 315 </when>
320 </conditional> 316 </conditional>
389 </conditional> 385 </conditional>
390 <conditional name="flavour"> 386 <conditional name="flavour">
391 <param name="type" value="mafft-fftns"/> 387 <param name="type" value="mafft-fftns"/>
392 </conditional> 388 </conditional>
393 <param name="outputFormat" value="--clustalout"/> 389 <param name="outputFormat" value="--clustalout"/>
394 <output name="outputAlignment" ftype="clustal" file="mafft_explicit_amino_blosum80.clustal.aln" /> 390 <output name="outputAlignment" ftype="clustal" file="mafft_explicit_amino_blosum80.clustal.aln" lines_diff="2" />
395 </test> 391 </test>
396 <test expect_num_outputs="1" > 392 <test expect_num_outputs="1" >
397 <conditional name="input"> 393 <conditional name="input">
398 <param name="mapping" value="implicit"/> 394 <param name="mapping" value="implicit"/>
399 <repeat name="batches"> 395 <repeat name="batches">
435 <section name="progressive_alignment_calculation"> 431 <section name="progressive_alignment_calculation">
436 <param name="maxiterate" value="1000"/> 432 <param name="maxiterate" value="1000"/>
437 </section> 433 </section>
438 </conditional> 434 </conditional>
439 <param name="outputFormat" value="--clustalout"/> 435 <param name="outputFormat" value="--clustalout"/>
440 <output name="outputAlignment" ftype="clustal" file="mafft_custom_original.clustal.aln"> 436 <output name="outputAlignment" ftype="clustal" file="mafft_custom_original.clustal.aln" lines_diff="2">
441 </output> 437 </output>
442 </test> 438 </test>
443 <test expect_num_outputs="1"> 439 <test expect_num_outputs="1">
444 <conditional name="input"> 440 <conditional name="input">
445 <param name="mapping" value="implicit"/> 441 <param name="mapping" value="implicit"/>