Mercurial > repos > bgruening > bionano_scaffold

comparison bionano_scaffold.xml @ 3:295c0e28f4ee draft

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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 8afc84a2ccaa084b4eedb01a0b76e4c463931db3"
author bgruening
date Sun, 23 May 2021 17:23:03 +0000
parents 9bd94d9a1b2e
children 8cc3862f8b8e
comparison
equal deleted inserted replaced
2:c612f2d2881c 3:295c0e28f4ee
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
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>perl /HybridScaffold/hybridScaffold.pl --version</version_command>
9 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
10 #set RefAligner = '/usr/local/bin/RefAligner' 9 #set RefAligner = '/usr/local/bin/RefAligner'
11 ## softlinks do not work 10 ## softlinks do not work
12 cp '${ngs_fasta}' ./ngs.fasta 11 cp '${ngs_fasta}' ./ngs.fasta
13 && cp '${bionano_cmap}' ./bionano.cmap 12 && cp '${bionano_cmap}' ./bionano.cmap
13 && export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024))
14 ## return max out of GALAXY_SLOTS and 2 --> use a minimum 2 slots
15 && export SLOTS=\$(( \${GALAXY_SLOTS:-2} > 2 ? \${GALAXY_SLOTS:-2} : 2 ))
14 #if $configuration_options.configuration == 'vgp' 16 #if $configuration_options.configuration == 'vgp'
15 && cp '${vgp_mode}' ./config.xml 17 && cp '${vgp_mode}' ./config.xml
18 && sed -i "s|__MEMORY__|\$GALAXY_MEMORY_GB|" ./config.xml
19 && sed -i "s|__CORES__|\$SLOTS|" ./config.xml
16 #else 20 #else
17 #import os
18 #set cores = os.environ.get('GALAXY_SLOTS', 2)
19 #set memory = os.environ.get('GALAXY_MEMORY_MB', 4000) / 1000
20 && cp '${configuration_file}' ./config.xml 21 && cp '${configuration_file}' ./config.xml
21 && sed -i 's|attr="maxmem" val0=.* display|attr="maxmem" val0="$memory" display|' ./config.xml 22 && sed -i "s|attr=\"maxmem\" val0=.* display|attr=\"maxmem\" val0=\"\$GALAXY_MEMORY_GB\" display|" ./config.xml
22 && sed -i 's|attr="maxthreads" val0=.* display|attr="maxthreads" val0="$cores" display|' ./config.xml 23 && sed -i "s|attr=\"maxthreads\" val0=.* display|attr=\"maxthreads\" val0=\"\$SLOTS\" display|" ./config.xml
23 && sed -i 's|attr="maxvirtmem" val0=.*/>|attr="maxvirtmem" val0="$cores"/>|' ./config.xml 24 && sed -i "s|attr=\"maxvirtmem\" val0=.*/>|attr=\"maxvirtmem\" val0=\"\$GALAXY_MEMORY_GB\"/>|" ./config.xml
24 && sed -i 's|attr="insertThreads" val0=.*/>|attr="insertThreads" val0="$cores"/>|' ./config.xml 25 && sed -i "s|attr=\"insertThreads\" val0=.*/>|attr=\"insertThreads\" val0=\"\$SLOTS\"/>|" ./config.xml
25 #end if 26 #end if
26 ## output the configuration file on stdout 27 ## output the configuration file on stdout
27 && cat ./config.xml 28 && cat ./config.xml
28 && perl '/HybridScaffold/hybridScaffold.pl' 29 && perl '/HybridScaffold/hybridScaffold.pl'
29 -n ./ngs.fasta 30 -n ./ngs.fasta
51 ## #end if 52 ## #end if
52 ###end if 53 ###end if
53 -f 54 -f
54 $zip_file 55 $zip_file
55 -o ./ 56 -o ./
56 ##;
57 ##sleep 1000000
58 57
59 ]]> </command> 58 ]]> </command>
60 <configfiles> 59 <configfiles>
61 <configfile name="vgp_mode"><![CDATA[ 60 <configfile name="vgp_mode"><![CDATA[
62 #if $configuration_options.configuration == 'vgp' 61 #if $configuration_options.configuration == 'vgp'
63 #import os
64 #set cores = os.environ.get('GALAXY_SLOTS', 2)
65 #set memory = os.environ.get('GALAXY_MEMORY_MB', 4000) / 1000
66 <hybridScaffold> 62 <hybridScaffold>
67 <version> 63 <version>
68 <flag attr="version" val0="\$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang \$"/> 64 <flag attr="version" val0="\$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang \$"/>
69 </version> 65 </version>
70 <global> 66 <global>
71 <flag attr="maxmem" val0="$memory" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/> 67 <flag attr="maxmem" val0="__MEMORY__" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>
72 <flag attr="maxthreads" val0="$cores" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/> 68 <flag attr="maxthreads" val0="__CORES__" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>
73 <flag attr="maxvirtmem" val0="$memory"/> 69 <flag attr="maxvirtmem" val0="__MEMORY__"/>
74 <flag attr="RAmem" val0="3" val1="1"/> 70 <flag attr="RAmem" val0="3" val1="1"/>
75 </global> 71 </global>
76 <fasta2cmap> 72 <fasta2cmap>
77 <flag attr="enzyme" val0="$configuration_options.enzyme" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Avalible enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/> 73 <flag attr="enzyme" val0="$configuration_options.enzyme" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Avalible enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/>
78 <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/> 74 <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/>
98 <flag attr="deltaY" val0="12"/> 94 <flag attr="deltaY" val0="12"/>
99 <flag attr="xmapchim" val0="12"/> 95 <flag attr="xmapchim" val0="12"/>
100 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/> 96 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
101 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/> 97 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
102 <flag attr="hashMultiMatch" val0="30" val1="10"/> 98 <flag attr="hashMultiMatch" val0="30" val1="10"/>
103 <flag attr="insertThreads" val0="$cores"/> 99 <flag attr="insertThreads" val0="__CORES__"/>
104 <flag attr="nosplit" val0="2"/> 100 <flag attr="nosplit" val0="2"/>
105 <flag attr="biaswt" val0="0"/> 101 <flag attr="biaswt" val0="0"/>
106 <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/> 102 <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
107 <flag attr="S" val0="-1000"/> 103 <flag attr="S" val0="-1000"/>
108 <flag attr="indel"/> 104 <flag attr="indel"/>
134 <flag attr="deltaY" val0="12"/> 130 <flag attr="deltaY" val0="12"/>
135 <flag attr="xmapchim" val0="12"/> 131 <flag attr="xmapchim" val0="12"/>
136 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/> 132 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
137 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/> 133 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
138 <flag attr="hashMultiMatch" val0="30" val1="10"/> 134 <flag attr="hashMultiMatch" val0="30" val1="10"/>
139 <flag attr="insertThreads" val0="$cores"/> 135 <flag attr="insertThreads" val0="__CORES__"/>
140 <flag attr="nosplit" val0="2"/> 136 <flag attr="nosplit" val0="2"/>
141 <flag attr="biaswt" val0="0"/> 137 <flag attr="biaswt" val0="0"/>
142 <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/> 138 <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
143 <flag attr="S" val0="-1000"/> 139 <flag attr="S" val0="-1000"/>
144 <flag attr="indel"/> 140 <flag attr="indel"/>
176 <flag attr="mres" val0="2.9" display=""/> 172 <flag attr="mres" val0="2.9" display=""/>
177 <flag attr="sf" val0="0.2" display=""/> 173 <flag attr="sf" val0="0.2" display=""/>
178 <flag attr="RepeatMask" val0="4" val1="0.01" display=""/> 174 <flag attr="RepeatMask" val0="4" val1="0.01" display=""/>
179 <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4" display=""/> 175 <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4" display=""/>
180 <flag attr="pairmerge" val0="80" val1="0.2" display="Min alignment length and Max endoutlier" group="Merging" description="Minimum alignment length required for pair merge, and the maximum endoutlier allowed."/> 176 <flag attr="pairmerge" val0="80" val1="0.2" display="Min alignment length and Max endoutlier" group="Merging" description="Minimum alignment length required for pair merge, and the maximum endoutlier allowed."/>
181 <flag attr="maxmem" val0="$memory" display=""/> 177 <flag attr="maxmem" val0="__MEMORY__" display=""/>
182 <flag attr="pairmergeRepeat"/> 178 <flag attr="pairmergeRepeat"/>
183 <flag attr="NoBpp"/> 179 <flag attr="NoBpp"/>
184 <flag attr="first" val0="-1" display=""/> 180 <flag attr="first" val0="-1" display=""/>
185 <flag attr="f"/> 181 <flag attr="f"/>
186 </mergeNGS_BN> 182 </mergeNGS_BN>
199 <flag attr="deltaY" val0="12"/> 195 <flag attr="deltaY" val0="12"/>
200 <flag attr="xmapchim" val0="12"/> 196 <flag attr="xmapchim" val0="12"/>
201 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/> 197 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
202 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/> 198 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
203 <flag attr="hashMultiMatch" val0="30" val1="10"/> 199 <flag attr="hashMultiMatch" val0="30" val1="10"/>
204 <flag attr="insertThreads" val0="$cores"/> 200 <flag attr="insertThreads" val0="__CORES__"/>
205 <flag attr="nosplit" val0="2"/> 201 <flag attr="nosplit" val0="2"/>
206 <flag attr="biaswt" val0="0"/> 202 <flag attr="biaswt" val0="0"/>
207 <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output intial alignments. Recommended starting value of 1e-5/genome size in Mb."/> 203 <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output intial alignments. Recommended starting value of 1e-5/genome size in Mb."/>
208 <flag attr="S" val0="-1000"/> 204 <flag attr="S" val0="-1000"/>
209 <flag attr="indel"/> 205 <flag attr="indel"/>
236 <flag attr="deltaY" val0="12"/> 232 <flag attr="deltaY" val0="12"/>
237 <flag attr="xmapchim" val0="12"/> 233 <flag attr="xmapchim" val0="12"/>
238 <flag attr="hashgen" val0="5" val1="3" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/> 234 <flag attr="hashgen" val0="5" val1="3" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
239 <flag attr="hash" val0="-hashdelta" val1="50"/> 235 <flag attr="hash" val0="-hashdelta" val1="50"/>
240 <flag attr="hashMultiMatch" val0="30" val1="10" val2="3"/> 236 <flag attr="hashMultiMatch" val0="30" val1="10" val2="3"/>
241 <flag attr="insertThreads" val0="$cores"/> 237 <flag attr="insertThreads" val0="__CORES__"/>
242 <flag attr="nosplit" val0="2"/> 238 <flag attr="nosplit" val0="2"/>
243 <flag attr="biaswt" val0="0"/> 239 <flag attr="biaswt" val0="0"/>
244 <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/> 240 <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/>
245 <flag attr="S" val0="-1000"/> 241 <flag attr="S" val0="-1000"/>
246 <flag attr="indel"/> 242 <flag attr="indel"/>
273 <flag attr="deltaY" val0="6"/> 269 <flag attr="deltaY" val0="6"/>
274 <flag attr="xmapchim" val0="12"/> 270 <flag attr="xmapchim" val0="12"/>
275 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/> 271 <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>
276 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/> 272 <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>
277 <flag attr="hashMultiMatch" val0="30" val1="10"/> 273 <flag attr="hashMultiMatch" val0="30" val1="10"/>
278 <flag attr="insertThreads" val0="$cores"/> 274 <flag attr="insertThreads" val0="__CORES__"/>
279 <flag attr="nosplit" val0="2"/> 275 <flag attr="nosplit" val0="2"/>
280 <flag attr="biaswt" val0="0"/> 276 <flag attr="biaswt" val0="0"/>
281 <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/> 277 <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/>
282 <flag attr="S" val0="-1000"/> 278 <flag attr="S" val0="-1000"/>
283 <flag attr="indel"/> 279 <flag attr="indel"/>
346 <flag attr="hashgen" val00="5" val01="3" val02="2.4" val03="1.5" val04="0.05" val05="5.0" val06="1" val07="1" val08="3"/> 342 <flag attr="hashgen" val00="5" val01="3" val02="2.4" val03="1.5" val04="0.05" val05="5.0" val06="1" val07="1" val08="3"/>
347 <flag attr="hash" val00="-hashdelta" val01="10" val02="10" val03="-mres" val04="0.9"/> 343 <flag attr="hash" val00="-hashdelta" val01="10" val02="10" val03="-mres" val04="0.9"/>
348 <flag attr="HSDrange" val0="1.0"/> 344 <flag attr="HSDrange" val0="1.0"/>
349 <flag attr="hashoffset" val0="1"/> 345 <flag attr="hashoffset" val0="1"/>
350 <flag attr="hashMultiMatch" val0="15"/> 346 <flag attr="hashMultiMatch" val0="15"/>
351 <flag attr="insertThreads" val0="$cores"/> 347 <flag attr="insertThreads" val0="__CORES__"/>
352 <flag attr="BestRef" val0="1"/> 348 <flag attr="BestRef" val0="1"/>
353 <flag attr="BestRefPV" val0="1"/> 349 <flag attr="BestRefPV" val0="1"/>
354 <flag attr="ChimQuality"/> 350 <flag attr="ChimQuality"/>
355 <flag attr="f" display="Overwrite Output Files" group="Final Refinement"/> 351 <flag attr="f" display="Overwrite Output Files" group="Final Refinement"/>
356 <flag attr="T" val0="1e-11" display="P Value Cutoff Threshold"/> 352 <flag attr="T" val0="1e-11" display="P Value Cutoff Threshold"/>
451 <!--<has_size value="4231746" delta="300" />--> 447 <!--<has_size value="4231746" delta="300" />-->
452 <has_archive_member path=".*/status.txt"/> 448 <has_archive_member path=".*/status.txt"/>
453 </assert_contents> 449 </assert_contents>
454 </output> 450 </output>
455 <assert_stdout> 451 <assert_stdout>
456 <has_text text='attr="maxmem" val0="4.0"'/> 452 <has_text text='attr="maxmem" val0="8"'/>
457 </assert_stdout> 453 </assert_stdout>
458 <assert_stdout> 454 <assert_stdout>
459 <has_text text='attr="maxthreads" val0="2"'/> 455 <has_text text='attr="maxthreads" val0="1"'/>
460 </assert_stdout> 456 </assert_stdout>
461 <assert_stdout> 457 <assert_stdout>
462 <has_text text='attr="insertThreads" val0="2"'/> 458 <has_text text='attr="insertThreads" val0="1"'/>
463 </assert_stdout> 459 </assert_stdout>
464 <assert_stdout> 460 <assert_stdout>
465 <has_text text='attr="maxvirtmem" val0="4.0"'/> 461 <has_text text='attr="maxvirtmem" val0="8"'/>
466 </assert_stdout> 462 </assert_stdout>
467 <assert_stdout> 463 <assert_stdout>
468 <has_text text="hybridScaffold"/> 464 <has_text text="hybridScaffold"/>
469 </assert_stdout> 465 </assert_stdout>
470 </test> 466 </test>
486 </output> 482 </output>
487 <output name="ngs_contigs_scaffold_agp" file="test_02.agp" ftype="txt"/> 483 <output name="ngs_contigs_scaffold_agp" file="test_02.agp" ftype="txt"/>
488 <output name="ngs_contigs_scaffold_gap" file="test_02.gap" ftype="txt"/> 484 <output name="ngs_contigs_scaffold_gap" file="test_02.gap" ftype="txt"/>
489 <output name="report" file="test_02_report.txt" ftype="txt"/> 485 <output name="report" file="test_02_report.txt" ftype="txt"/>
490 <assert_stdout> 486 <assert_stdout>
491 <has_text text='attr="maxmem" val0="4.0"'/> 487 <has_text text='attr="maxmem" val0="8"'/>
492 </assert_stdout> 488 </assert_stdout>
493 <assert_stdout> 489 <assert_stdout>
494 <has_text text='attr="maxthreads" val0="2"'/> 490 <has_text text='attr="maxthreads" val0="1"'/>
495 </assert_stdout> 491 </assert_stdout>
496 <assert_stdout> 492 <assert_stdout>
497 <has_text text='attr="insertThreads" val0="2"'/> 493 <has_text text='attr="insertThreads" val0="1"'/>
498 </assert_stdout> 494 </assert_stdout>
499 <assert_stdout> 495 <assert_stdout>
500 <has_text text='attr="maxvirtmem" val0="4.0"'/> 496 <has_text text='attr="maxvirtmem" val0="8"'/>
501 </assert_stdout> 497 </assert_stdout>
502 <assert_stdout> 498 <assert_stdout>
503 <has_text text="hybridScaffold"/> 499 <has_text text="hybridScaffold"/>
504 <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/--> 500 <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/-->
505 </assert_stdout> 501 </assert_stdout>
529 <!--<has_size value="4231908" delta="300" />--> 525 <!--<has_size value="4231908" delta="300" />-->
530 <has_archive_member path=".*/status.txt"/> 526 <has_archive_member path=".*/status.txt"/>
531 </assert_contents> 527 </assert_contents>
532 </output> 528 </output>
533 <assert_stdout> 529 <assert_stdout>
534 <has_text text='attr="maxmem" val0="4.0"'/> 530 <has_text text='attr="maxmem" val0="8"'/>
535 </assert_stdout> 531 </assert_stdout>
536 <assert_stdout> 532 <assert_stdout>
537 <has_text text='attr="maxthreads" val0="2"'/> 533 <has_text text='attr="maxthreads" val0="1"'/>
538 </assert_stdout> 534 </assert_stdout>
539 <assert_stdout> 535 <assert_stdout>
540 <has_text text='attr="insertThreads" val0="2"'/> 536 <has_text text='attr="insertThreads" val0="1"'/>
541 </assert_stdout> 537 </assert_stdout>
542 <assert_stdout> 538 <assert_stdout>
543 <has_text text='attr="maxvirtmem" val0="4.0"'/> 539 <has_text text='attr="maxvirtmem" val0="8"'/>
544 </assert_stdout> 540 </assert_stdout>
545 <assert_stdout> 541 <assert_stdout>
546 <has_text text="hybridScaffold"/> 542 <has_text text="hybridScaffold"/>
547 </assert_stdout> 543 </assert_stdout>
548 </test> 544 </test>
570 <assert_contents> 566 <assert_contents>
571 <has_archive_member path=".*/status.txt"/> 567 <has_archive_member path=".*/status.txt"/>
572 </assert_contents> 568 </assert_contents>
573 </output> 569 </output>
574 <assert_stdout> 570 <assert_stdout>
575 <has_text text='attr="maxmem" val0="4.0"'/> 571 <has_text text='attr="maxmem" val0="8"'/>
576 </assert_stdout> 572 </assert_stdout>
577 <assert_stdout> 573 <assert_stdout>
578 <has_text text='attr="maxthreads" val0="2"'/> 574 <has_text text='attr="maxthreads" val0="1"'/>
579 </assert_stdout> 575 </assert_stdout>
580 <assert_stdout> 576 <assert_stdout>
581 <has_text text='attr="insertThreads" val0="2"'/> 577 <has_text text='attr="insertThreads" val0="1"'/>
582 </assert_stdout> 578 </assert_stdout>
583 <assert_stdout> 579 <assert_stdout>
584 <has_text text='attr="maxvirtmem" val0="4.0"'/> 580 <has_text text='attr="maxvirtmem" val0="8"'/>
585 </assert_stdout> 581 </assert_stdout>
586 <assert_stdout> 582 <assert_stdout>
587 <has_text text="hybridScaffold"/> 583 <has_text text="hybridScaffold"/>
588 </assert_stdout> 584 </assert_stdout>
589 </test> 585 </test>