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comparison meryl.xml @ 5:d63739222f68 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c"
author iuc
date Sun, 23 May 2021 18:09:41 +0000
parents d5d68989caec
children 31fa26c0692b
comparison
equal deleted inserted replaced
4:d5d68989caec 5:d63739222f68
5 </macros> 5 </macros>
6 <expand macro='edam_ontology' /> 6 <expand macro='edam_ontology' />
7 <expand macro='requirements' /> 7 <expand macro='requirements' />
8 <version_command>meryl --version</version_command> 8 <version_command>meryl --version</version_command>
9 <command detect_errors='exit_code'><![CDATA[ 9 <command detect_errors='exit_code'><![CDATA[
10 export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
10 #if $operation_type.command_type == 'count-kmers' 11 #if $operation_type.command_type == 'count-kmers'
11 #if $operation_type.options_kmer_size.kmer_size == 'estimate' 12 #if $operation_type.options_kmer_size.kmer_size == 'estimate'
12 #from math import log 13 #from math import log
13 #set size=int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4)) 14 #set size=int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4))
14 #elif $operation_type.options_kmer_size.kmer_size == 'provide' 15 #elif $operation_type.options_kmer_size.kmer_size == 'provide'
15 #set size=$operation_type.options_kmer_size.input_kmer_size 16 #set size=$operation_type.options_kmer_size.input_kmer_size
16 #end if 17 #end if
17 meryl 18 meryl
18 $operation_type.count_operations 19 $operation_type.count_operations
19 k=$size 20 k=$size
20 memory=\${GALAXY_MEMORY_GB:-1} 21 memory=\$GALAXY_MEMORY_GB
21 threads=\${GALAXY_SLOTS:-1} 22 threads=\${GALAXY_SLOTS:-1}
22 $operation_type.input_reads 23 $operation_type.input_reads
23 output read-db.meryl && 24 output read-db.meryl &&
24 echo 'K-mer size: ${size}' && 25 echo 'K-mer size: ${size}' &&
25 tar -zcf read-db.meryldb read-db.meryl 26 tar -zcf read-db.meryldb read-db.meryl
77 #elif $operation_type.options_kmer_size.kmer_size == 'provide' 78 #elif $operation_type.options_kmer_size.kmer_size == 'provide'
78 #set size=$operation_type.options_kmer_size.input_kmer_size 79 #set size=$operation_type.options_kmer_size.input_kmer_size
79 #end if 80 #end if
80 #for $i, $read in enumerate($paternal_reads): 81 #for $i, $read in enumerate($paternal_reads):
81 mkdir 'paternal{$i}.meryl' && 82 mkdir 'paternal{$i}.meryl' &&
82 meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'paternal{$i}.meryl' && 83 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'paternal{$i}.meryl' &&
83 #end for 84 #end for
84 meryl union-sum paternal*.meryl output pat.meryl && 85 meryl union-sum paternal*.meryl output pat.meryl &&
85 #for $i, $read in enumerate($maternal_reads): 86 #for $i, $read in enumerate($maternal_reads):
86 mkdir 'maternal{$i}.meryl' && 87 mkdir 'maternal{$i}.meryl' &&
87 meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'maternal{$i}.meryl' && 88 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'maternal{$i}.meryl' &&
88 #end for 89 #end for
89 meryl union-sum maternal*.meryl output mat.meryl && 90 meryl union-sum maternal*.meryl output mat.meryl &&
90 #for $i, $read in enumerate($child_reads): 91 #for $i, $read in enumerate($child_reads):
91 mkdir 'child{$i}.meryl' && 92 mkdir 'child{$i}.meryl' &&
92 meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'child{$i}.meryl' && 93 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'child{$i}.meryl' &&
93 #end for 94 #end for
94 meryl union-sum child*.meryl output child.meryl && 95 meryl union-sum child*.meryl output child.meryl &&
95 ## mat specific kmers 96 ## mat specific kmers
96 meryl difference mat.meryl pat.meryl output mat.only.meryl && 97 meryl difference mat.meryl pat.meryl output mat.only.meryl &&
97 meryl histogram mat.only.meryl > mat.only.hist && 98 meryl histogram mat.only.meryl > mat.only.hist &&
142 <inputs> 143 <inputs>
143 <conditional name="operation_type"> 144 <conditional name="operation_type">
144 <param name="command_type" type="select" label="Operation type selector" help="Select a type of operation"> 145 <param name="command_type" type="select" label="Operation type selector" help="Select a type of operation">
145 <option value="count-kmers">Count operations</option> 146 <option value="count-kmers">Count operations</option>
146 <option value="filter-kmers">Filter operations</option> 147 <option value="filter-kmers">Filter operations</option>
147 <option value="arithmetic-kmers">Arithmetic operations on kmer counts</option> 148 <option value="arithmetic-kmers">Arithmetic operations on k-mer counts</option>
148 <option value="groups-kmers">Operations on sets of k-mers</option> 149 <option value="groups-kmers">Operations on sets of k-mers</option>
149 <option value="histogram-kmers">Generate histogram dataset</option> 150 <option value="histogram-kmers">Generate histogram dataset</option>
150 <option value="print">Print kmer counts to a tabular file</option> 151 <option value="print">Print k-mer counts to a tabular file</option>
151 <option value="trio-mode">Build hap-mer dbs for trios</option> 152 <option value="trio-mode">Build hap-mer dbs for trios</option>
152 </param> 153 </param>
153 <when value="count-kmers"> 154 <when value="count-kmers">
154 <param name="count_operations" type="select" label="Count operations" help="Select an operation to be executed"> 155 <param name="count_operations" type="select" label="Count operations" help="Select an operation to be executed">
155 <option value="count">Count: count the occurrences of canonical k-mers</option> 156 <option value="count">Count: count the occurrences of canonical k-mers</option>
180 </param> 181 </param>
181 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" /> 182 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" />
182 183
183 <conditional name="filter_type"> 184 <conditional name="filter_type">
184 <param name="type" type="select" label="Type of filtering"> 185 <param name="type" type="select" label="Type of filtering">
185 <option value="times">Return kmers that occur N times in the input</option> 186 <option value="times">Return k-mers that occur N times in the input</option>
186 <option value="frequency">Return kmers occurring at specific frequencies</option> 187 <option value="frequency">Return k-mers occurring at specific frequencies</option>
187 </param> 188 </param>
188 <when value="times"> 189 <when value="times">
189 <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Number of times in the input" help="Return kmers that occur N times in the input."/> 190 <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Number of times in the input" help="Return k-mers that occur N times in the input."/>
190 </when> 191 </when>
191 <when value="frequency"> 192 <when value="frequency">
192 <param name="distinct" type="float" min="0" max="1" value="0.9998" optional="true" label="Frequency" help="Return kmers that at specific frequency (e.g. frequency = 0.9998 returns top 0.02% most frequent)"/> 193 <param name="distinct" type="float" min="0" max="1" value="0.9998" optional="true" label="Frequency" help="Return k-mers that at specific frequency (e.g. frequency = 0.9998 returns top 0.02% most frequent)"/>
193 </when> 194 </when>
194 </conditional> 195 </conditional>
195 </when> 196 </when>
196 <when value="arithmetic-kmers"> 197 <when value="arithmetic-kmers">
197 <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed"> 198 <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed">
198 <option value="increase">Increase: add x to the count of each k-mer</option> 199 <option value="increase">Increase: add x to the count of each k-mer</option>
199 <option value="decrease">Decrease: subsctract x from the count of each k-mer</option> 200 <option value="decrease">Decrease: subtract x from the count of each k-mer</option>
200 <option value="multiply">Multiply: multiply the count of each k-mer by x</option> 201 <option value="multiply">Multiply: multiply the count of each k-mer by x</option>
201 <option value="divide">Divide: divide the count of each k-mer by x</option> 202 <option value="divide">Divide: divide the count of each k-mer by x</option>
202 <option value="divide-round">Divide-round: divide the count of each k-mer by x and round th results</option> 203 <option value="divide-round">Divide-round: divide the count of each k-mer by x and round th results</option>
203 <option value="modulo">Modulo: set the count of each k-mer to the remainder of the count divided by x</option> 204 <option value="modulo">Modulo: set the count of each k-mer to the remainder of the count divided by x</option>
204 </param> 205 </param>
205 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" /> 206 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" />
206 <param name="X" type="integer" min="1" max="1000000" value="" optional="true" label="Operand" /> 207 <param name="X" type="integer" min="1" max="1000000" value="" optional="true" label="Operand" />
207 </when> 208 </when>
208 <when value="groups-kmers"> 209 <when value="groups-kmers">
209 <param name="groups_operations" type="select" label="Operations on sets of kmers" help="Select an operation to be executed"> 210 <param name="groups_operations" type="select" label="Operations on sets of k-mers" help="Select an operation to be executed">
210 <option value="union">Union: return k-mers that occur in any input</option> 211 <option value="union">Union: return k-mers that occur in any input</option>
211 <option value="union-min">Union-min: return k-mers that occur in any input, set the count to the minimum count</option> 212 <option value="union-min">Union-min: return k-mers that occur in any input, set the count to the minimum count</option>
212 <option value="union-max">Union-max: return k-mers that occur in any input, set the count to the maximum count</option> 213 <option value="union-max">Union-max: return k-mers that occur in any input, set the count to the maximum count</option>
213 <option value="union-sum">Union-sum: return k-mers that occur in any input, set the count to the sum of the counts</option> 214 <option value="union-sum">Union-sum: return k-mers that occur in any input, set the count to the sum of the counts</option>
214 <option value="intersect">Intersect: return k-mers that occur in all inputs, set the count to the count in the first input</option> 215 <option value="intersect">Intersect: return k-mers that occur in all inputs, set the count to the count in the first input</option>
360 <param name="N" value="100" /> 361 <param name="N" value="100" />
361 </conditional> 362 </conditional>
362 </conditional> 363 </conditional>
363 <output name="read_db" ftype="meryldb"> 364 <output name="read_db" ftype="meryldb">
364 <assert_contents> 365 <assert_contents>
365 <has_size value="59378" delta="300" /> 366 <has_size value="59100" delta="300" />
366 </assert_contents> 367 </assert_contents>
367 </output> 368 </output>
368 </test> 369 </test>
369 <test expect_num_outputs="1"> 370 <test expect_num_outputs="1">
370 <conditional name="operation_type"> 371 <conditional name="operation_type">
373 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> 374 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
374 <param name="X" value="100000" /> 375 <param name="X" value="100000" />
375 </conditional> 376 </conditional>
376 <output name="read_db" ftype="meryldb"> 377 <output name="read_db" ftype="meryldb">
377 <assert_contents> 378 <assert_contents>
378 <has_size value="59822" delta="300" /> 379 <has_size value="59500" delta="300" />
379 </assert_contents> 380 </assert_contents>
380 </output> 381 </output>
381 </test> 382 </test>
382 <test expect_num_outputs="1"> 383 <test expect_num_outputs="1">
383 <conditional name="operation_type"> 384 <conditional name="operation_type">
399 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> 400 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
400 <param name="X" value="3" /> 401 <param name="X" value="3" />
401 </conditional> 402 </conditional>
402 <output name="read_db" ftype="meryldb"> 403 <output name="read_db" ftype="meryldb">
403 <assert_contents> 404 <assert_contents>
404 <has_size value="60531" delta="300" /> 405 <has_size value="60530" delta="300" />
405 </assert_contents> 406 </assert_contents>
406 </output> 407 </output>
407 </test> 408 </test>
408 <test expect_num_outputs="1"> 409 <test expect_num_outputs="1">
409 <conditional name="operation_type"> 410 <conditional name="operation_type">
412 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> 413 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
413 <param name="X" value="2" /> 414 <param name="X" value="2" />
414 </conditional> 415 </conditional>
415 <output name="read_db" ftype="meryldb"> 416 <output name="read_db" ftype="meryldb">
416 <assert_contents> 417 <assert_contents>
417 <has_size value="56569" delta="300" /> 418 <has_size value="56200" delta="300" />
418 </assert_contents> 419 </assert_contents>
419 </output> 420 </output>
420 </test> 421 </test>
421 <test expect_num_outputs="1"> 422 <test expect_num_outputs="1">
422 <conditional name="operation_type"> 423 <conditional name="operation_type">
425 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> 426 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
426 <param name="X" value="2" /> 427 <param name="X" value="2" />
427 </conditional> 428 </conditional>
428 <output name="read_db" ftype="meryldb"> 429 <output name="read_db" ftype="meryldb">
429 <assert_contents> 430 <assert_contents>
430 <has_size value="56539" delta="300" /> 431 <has_size value="56100" delta="300" />
431 </assert_contents> 432 </assert_contents>
432 </output> 433 </output>
433 </test> 434 </test>
434 <!-- test 11 --> 435 <!-- test 11 -->
435 <test expect_num_outputs="1"> 436 <test expect_num_outputs="1">
452 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 453 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
453 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> 454 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
454 </conditional> 455 </conditional>
455 <output name="read_db" ftype="meryldb"> 456 <output name="read_db" ftype="meryldb">
456 <assert_contents> 457 <assert_contents>
457 <has_size value="36417" delta="300" /> 458 <has_size value="36100" delta="300" />
458 </assert_contents> 459 </assert_contents>
459 </output> 460 </output>
460 </test> 461 </test>
461 <test expect_num_outputs="1"> 462 <test expect_num_outputs="1">
462 <conditional name="operation_type"> 463 <conditional name="operation_type">
491 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 492 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
492 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> 493 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
493 </conditional> 494 </conditional>
494 <output name="read_db" ftype="meryldb"> 495 <output name="read_db" ftype="meryldb">
495 <assert_contents> 496 <assert_contents>
496 <has_size value="59004" delta="350" /> 497 <has_size value="58600" delta="300" />
497 </assert_contents> 498 </assert_contents>
498 </output> 499 </output>
499 </test> 500 </test>
500 <test expect_num_outputs="1"> 501 <test expect_num_outputs="1">
501 <conditional name="operation_type"> 502 <conditional name="operation_type">