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comparison canu.xml @ 2:c5b7390290b1 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit ecd77cd558a9b941fd0dfb71c4e534feba3ee7da
author bgruening
date Sun, 26 May 2019 10:52:09 -0400
parents 58346ef3116b
children 5732f959936a
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1:58346ef3116b 2:c5b7390290b1
1 <tool id="canu" name="Canu assembler" version="1.7"> 1 <tool id="canu" name="Canu assembler" version="1.8">
2 <description>Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore </description> 2 <description>Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore </description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.7">canu</requirement> 4 <requirement type="package" version="1.8">canu</requirement>
5 </requirements> 5 </requirements>
6 <version_command>canu --version</version_command> 6 <version_command>canu --version</version_command>
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
8 <![CDATA[ 8 <![CDATA[
9 9
39 ${contigFilter.singleReadSpan} 39 ${contigFilter.singleReadSpan}
40 ${contigFilter.lowCovSpan} 40 ${contigFilter.lowCovSpan}
41 ${contigFilter.lowCovDepth} 41 ${contigFilter.lowCovDepth}
42 ' 42 '
43 genomeSize=$genomeSize 43 genomeSize=$genomeSize
44 stopOnReadQuality=false
45 minThreads=\${GALAXY_SLOTS:-4} 44 minThreads=\${GALAXY_SLOTS:-4}
46 maxThreads=\${GALAXY_SLOTS:-4} 45 maxThreads=\${GALAXY_SLOTS:-4}
47 obtovlThreads=\${GALAXY_SLOTS:-4} 46 obtovlThreads=\${GALAXY_SLOTS:-4}
48 utgovlThreads=\${GALAXY_SLOTS:-4} 47 utgovlThreads=\${GALAXY_SLOTS:-4}
49 batThreads=\${GALAXY_SLOTS:-4} 48 batThreads=\${GALAXY_SLOTS:-4}
50 batMemory=\${GALAXY_MEMORY_MB:-7} 49 batMemory=\${GALAXY_MEMORY_MB:-4096}M
51 cormhapMemory=\${GALAXY_MEMORY_MB:-7} 50 cormhapMemory=\${GALAXY_MEMORY_MB:-4096}M
52 obtovlMemory=\${GALAXY_MEMORY_MB:-7} 51 obtovlMemory=\${GALAXY_MEMORY_MB:-4096}M
53 utgovlMemory=\${GALAXY_MEMORY_MB:-7} 52 utgovlMemory=\${GALAXY_MEMORY_MB:-4096}M
54 gfaThreads=\${GALAXY_SLOTS:-4} 53 gfaThreads=\${GALAXY_SLOTS:-4}
55 corThreads=\${GALAXY_SLOTS:-4} 54 corThreads=\${GALAXY_SLOTS:-4}
56 cnsThreads=\${GALAXY_SLOTS:-4} 55 cnsThreads=\${GALAXY_SLOTS:-4}
57 gnuplotTested=true
58 useGrid=false 56 useGrid=false
59 $mode 57 $mode
60 #for $counter, $input in enumerate($inputs): 58 #for $counter, $input in enumerate($inputs):
61 #if $input.ext in ['fastq.gz', 'fasta.gz'] 59 #if $input.ext in ['fastq.gz', 'fasta.gz']
62 ./input_${counter}.gz 60 ./input_${counter}.gz