Mercurial > repos > iuc > meryl
comparison meryl.xml @ 8:5ae3496f9ca3 draft
"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> |