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comparison mafft.xml @ 14:6f28e90db932 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 1570f3a28232b4b88385cdfbb68f79d80ff1dabb
author bgruening
date Tue, 31 Oct 2023 15:48:53 +0000
parents 4de39704d423
children bf28a8cff401
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13:a65296ffb4a0 14:6f28e90db932
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="rbc_mafft" name="MAFFT" version="@TOOL_VERSION@+galaxy@VERSION@"> 2 <tool id="rbc_mafft" name="MAFFT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>Multiple alignment program for amino acid or nucleotide sequences</description> 3 <description>Multiple alignment program for amino acid or nucleotide sequences</description>
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="requirements" /> 8 <expand macro="requirements" />
8 <stdio> 9 <stdio>
9 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> 10 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
10 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> 11 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
11 </stdio> 12 </stdio>
227 <param name="inputSequences" value="sample.fa"/> 228 <param name="inputSequences" value="sample.fa"/>
228 <param name="flavourType" value="mafft-nwns"/> 229 <param name="flavourType" value="mafft-nwns"/>
229 <param name="outputFormat" value="--clustalout"/> 230 <param name="outputFormat" value="--clustalout"/>
230 <output name="outputAlignment" ftype="clustal" file="mafft_nwns_result.aln" lines_diff="2" /> 231 <output name="outputAlignment" ftype="clustal" file="mafft_nwns_result.aln" lines_diff="2" />
231 </test> 232 </test>
233 <!-- WARNING: the results of the following test depends on #threads.
234 The result seems deterministic for single threaded execution, i.e. GALAXY_SLOTS=1 planemo test
235 However, GH CI/CD uses 2 threads and results vary -->
232 <test expect_num_outputs="1" > 236 <test expect_num_outputs="1" >
233 <param name="inputSequences" value="sample.fa"/> 237 <param name="inputSequences" value="sample.fa"/>
234 <param name="flavourType" value="custom"/> 238 <param name="flavourType" value="custom"/>
235 <param name="matrix_condition" value="BLOSUM"/> 239 <conditional name="matrix_condition">
240 <param name="matrix" value="BLOSUM"/>
241 </conditional>
236 <param name="BLOSUM" value="62"/> 242 <param name="BLOSUM" value="62"/>
237 <param name="distance_method" value="--fastapair"/> 243 <param name="distance_method" value="--fastapair"/>
238 <param name="weighti" value="2.7"/> 244 <param name="weighti" value="2.7"/>
239 <param name="iterations" value="1000"/> 245 <param name="iterations" value="1000"/>
240 <param name="outputFormat" value="--clustalout"/> 246 <param name="outputFormat" value="--clustalout"/>
241 <output name="outputAlignment" ftype="clustal" file="mafft_custom_result.aln" lines_diff="2" /> 247 <output name="outputAlignment" ftype="clustal" file="mafft_custom_result.aln" compare="sim_size">
248 <assert_contents>
249 <has_n_lines n="458" delta="0"/>
250 <has_text text="CLUSTAL format alignment by MAFFT F-INS-i"/>
251 <has_text text="NPIVYGISHPKY"/>
252 <has_text text="1=="/>
253 <has_text text="36=="/>
254 <has_line line="8=opsin, ------------------------------------------------------------"/>
255 </assert_contents>
256 </output>
242 </test> 257 </test>
243 </tests> 258 </tests>
244 <help> <![CDATA[ 259 <help> <![CDATA[
245 **What it does** 260 **What it does**
261
246 MAFFT is a multiple sequence alignment program for unix-like operating systems. 262 MAFFT is a multiple sequence alignment program for unix-like operating systems.
247 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), 263 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),
248 FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. 264 FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
249 From the MAFFT man page, an overview of the different predefined flavours of the tool. 265 From the MAFFT man page, an overview of the different predefined flavours of the tool is as follows:
266
250 **Accuracy-oriented methods:** 267 **Accuracy-oriented methods:**
268
251 - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information): 269 - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
252 - mafft --localpair --maxiterate 1000 input [> output] 270 - mafft --localpair --maxiterate 1000 input [> output]
253 - G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information): 271 - G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
254 - mafft --globalpair --maxiterate 1000 input [> output] 272 - mafft --globalpair --maxiterate 1000 input [> output]
255 - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences): 273 - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
256 - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps. 274 - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps.
275
257 **Speed-oriented methods:** 276 **Speed-oriented methods:**
277
258 - FFT-NS-i (iterative refinement method; two cycles only): 278 - FFT-NS-i (iterative refinement method; two cycles only):
259 - mafft --retree 2 --maxiterate 2 input [> output] 279 - mafft --retree 2 --maxiterate 2 input [> output]
260 - FFT-NS-i (iterative refinement method; max. 1000 iterations): 280 - FFT-NS-i (iterative refinement method; max. 1000 iterations):
261 - mafft --retree 2 --maxiterate 1000 input [> output] 281 - mafft --retree 2 --maxiterate 1000 input [> output]
262 - FFT-NS-2 (fast; progressive method): 282 - FFT-NS-2 (fast; progressive method):
269 - mafft --retree 2 --maxiterate 0 --nofft input [> output] 289 - mafft --retree 2 --maxiterate 0 --nofft input [> output]
270 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm): 290 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
271 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output] 291 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
272 292
273 **Options:** 293 **Options:**
274 --auto 294
275 Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2) 295 - --auto Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
276 --adjustdirection 296 - --adjustdirection Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored.
277 Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored. 297 - --op Gap opening penalty, default: 1.53
278 --op 298 - --ep Offset (works like gap extension penalty), default: 0.0
279 Gap opening penalty, default: 1.53 299 - --maxiterate Maximum number of iterative refinement, default: 0
280 --ep 300 - --clustalout Output: clustal format, default: fasta
281 Offset (works like gap extension penalty), default: 0.0 301 - --retree number Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2
282 --maxiterate
283 Maximum number of iterative refinement, default: 0
284 --clustalout
285 Output: clustal format, default: fasta
286 --thread
287 Number of threads (if unsure, --thread -1)
288 --retree number
289 Guide tree is built number times in the progressive stage.
290 Valid with 6mer distance. Default: 2
291 ]]> 302 ]]>
292 </help> 303 </help>
293 <expand macro="citations" /> 304 <expand macro="citations" />
294 </tool> 305 </tool>