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comparison meryl.xml @ 8:5ae3496f9ca3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20"
author iuc
date Thu, 12 Aug 2021 13:20:54 +0000
parents 51c2360aa807
children eadfd71dde37
comparison
equal deleted inserted replaced
7:51c2360aa807 8:5ae3496f9ca3
13 #from math import log 13 #from math import log
14 #set size=int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4)) 14 #set size=int(log(int($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))
15 #elif $operation_type.options_kmer_size.kmer_size == 'provide' 15 #elif $operation_type.options_kmer_size.kmer_size == 'provide'
16 #set size=$operation_type.options_kmer_size.input_kmer_size 16 #set size=$operation_type.options_kmer_size.input_kmer_size
17 #end if 17 #end if
18 ln -s '$operation_type.input_reads' ./input.${operation_type.input_reads.ext} &&
19
18 meryl 20 meryl
19 $operation_type.count_operations 21 $operation_type.count_operations
20 k=$size 22 k=$size
21 memory=\$GALAXY_MEMORY_GB 23 memory=\$GALAXY_MEMORY_GB
22 threads=\${GALAXY_SLOTS:-1} 24 threads=\${GALAXY_SLOTS:-1}
23 $operation_type.input_reads 25 ./input.${operation_type.input_reads.ext}
24 output read-db.meryl && 26 output read-db.meryl &&
25 echo 'K-mer size: ${size}' && 27 echo 'K-mer size: ${size}' &&
26 tar -zcf read-db.meryldb read-db.meryl 28 tar -zcf read-db.meryldb read-db.meryl
27 #elif $operation_type.command_type == 'filter-kmers' 29 #elif $operation_type.command_type == 'filter-kmers'
28 mkdir -p ./temp_db/ && 30 mkdir -p ./temp_db/ &&
174 <option value="greater-than">Greater-than: return k-mers that occur more than a threshold value</option> 176 <option value="greater-than">Greater-than: return k-mers that occur more than a threshold value</option>
175 <option value="equal-to">Equal-to: return k-mers that occur exactly a threshold value</option> 177 <option value="equal-to">Equal-to: return k-mers that occur exactly a threshold value</option>
176 <option value="not-equal-to">Not-equal-to: return k-mers that do not occur exactly a threshold value</option> 178 <option value="not-equal-to">Not-equal-to: return k-mers that do not occur exactly a threshold value</option>
177 </param> 179 </param>
178 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" /> 180 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" />
179 181
180 <conditional name="filter_type"> 182 <conditional name="filter_type">
181 <param name="type" type="select" label="Type of filtering"> 183 <param name="type" type="select" label="Type of filtering">
182 <option value="times">Return k-mers that occur N times in the input</option> 184 <option value="times">Return k-mers that occur N times in the input</option>
183 <option value="frequency">Return k-mers occurring at specific frequencies</option> 185 <option value="frequency">Return k-mers occurring at specific frequencies</option>
184 </param> 186 </param>
185 <when value="times"> 187 <when value="times">
186 <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."/> 188 <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." />
187 </when> 189 </when>
188 <when value="frequency"> 190 <when value="frequency">
189 <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)"/> 191 <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)" />
190 </when> 192 </when>
191 </conditional> 193 </conditional>
192 </when> 194 </when>
193 <when value="arithmetic-kmers"> 195 <when value="arithmetic-kmers">
194 <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed"> 196 <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed">
324 <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" /> 326 <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" />
325 <conditional name="filter_type"> 327 <conditional name="filter_type">
326 <param name="distinct" value="0.9998" /> 328 <param name="distinct" value="0.9998" />
327 </conditional> 329 </conditional>
328 </conditional> 330 </conditional>
329 <output name="read_db" ftype="meryldb" > 331 <output name="read_db" ftype="meryldb">
330 <assert_contents> 332 <assert_contents>
331 <has_size value="1634" delta="300" /> 333 <has_size value="1634" delta="300" />
332 </assert_contents> 334 </assert_contents>
333 </output> 335 </output>
334 </test> 336 </test>
341 <param name="N" value="100" /> 343 <param name="N" value="100" />
342 </conditional> 344 </conditional>
343 </conditional> 345 </conditional>
344 <output name="read_db" ftype="meryldb"> 346 <output name="read_db" ftype="meryldb">
345 <assert_contents> 347 <assert_contents>
346 <has_size value="2621" delta="300"/> 348 <has_size value="2621" delta="300" />
347 </assert_contents> 349 </assert_contents>
348 </output> 350 </output>
349 </test> 351 </test>
350 <test expect_num_outputs="1"> 352 <test expect_num_outputs="1">
351 <conditional name="operation_type"> 353 <conditional name="operation_type">
615 <test expect_num_outputs="1"> 617 <test expect_num_outputs="1">
616 <conditional name="operation_type"> 618 <conditional name="operation_type">
617 <param name="command_type" value="print" /> 619 <param name="command_type" value="print" />
618 <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" /> 620 <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" />
619 </conditional> 621 </conditional>
620 <output name="read_db_print" file="output_25.read-db.tabular" sort="True"/> 622 <output name="read_db_print" file="output_25.read-db.tabular" sort="true" />
621 </test> 623 </test>
622 <!--Test compressed files--> 624 <!--Test compressed files-->
623 <test expect_num_outputs="1"> 625 <test expect_num_outputs="1">
624 <conditional name="operation_type"> 626 <conditional name="operation_type">
625 <param name="command_type" value="count-kmers" /> 627 <param name="command_type" value="count-kmers" />
626 <param name="count_operation" value="count" /> 628 <param name="count_operation" value="count" />
627 <param name="input_reads" value="child.fasta.gz" /> 629 <param name="input_reads" value="child.fasta.gz" ftype="fasta.gz" />
628 <conditional name="options_kmer_size"> 630 <conditional name="options_kmer_size">
629 <param name="kmer_size" value="provide" /> 631 <param name="kmer_size" value="provide" />
630 <param name="input_kmer_size" value="7" /> 632 <param name="input_kmer_size" value="7" />
631 </conditional> 633 </conditional>
632 </conditional> 634 </conditional>
633 <output name="read_db" ftype="meryldb"> 635 <output name="read_db" ftype="meryldb">
634 <assert_contents> 636 <assert_contents>
635 <has_size value="1851" delta="300" /> 637 <has_size value="22200" delta="300" />
636 </assert_contents> 638 </assert_contents>
637 </output> 639 </output>
638 <assert_stdout> 640 <assert_stdout>
639 <has_line line="K-mer size: 7" /> 641 <has_line line="K-mer size: 7" />
640 </assert_stdout> 642 </assert_stdout>