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comparison canu.xml @ 2:a5198537f8a2 draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/canu commit da020fbee6e2bd91bc4a8d0850dc601db34ac82b-dirty
author jdv
date Sun, 15 Oct 2017 22:29:50 -0400
parents ed5df116fad3
children
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1:ed5df116fad3 2:a5198537f8a2
29 rawErrorRate=$rawErrorRate 29 rawErrorRate=$rawErrorRate
30 correctedErrorRate=$correctedErrorRate 30 correctedErrorRate=$correctedErrorRate
31 minReadLength=$minReadLength 31 minReadLength=$minReadLength
32 minOverlapLength=$minOverlapLength 32 minOverlapLength=$minOverlapLength
33 corOutCoverage=$corOutCoverage 33 corOutCoverage=$corOutCoverage
34 contigFilter="
35 ${contigFilter.minReads}
36 ${contigFilter.minLength}
37 ${contigFilter.singleReadSpan}
38 ${contigFilter.lowCovSpan}
39 ${contigFilter.lowCovDepth}
40 "
34 minThreads=\${GALAXY_SLOTS:-1} 41 minThreads=\${GALAXY_SLOTS:-1}
35 maxThreads=\${GALAXY_SLOTS:-1} 42 maxThreads=\${GALAXY_SLOTS:-1}
36 gnuplotTested=true 43 gnuplotTested=true
37 useGrid=false 44 useGrid=false
38 $mode 45 $mode
57 <param argument="rawErrorRate" type="float" value="0.500" min="0" max="1" size="5" label="Maximum raw overlap mismatch (0-1)" /> 64 <param argument="rawErrorRate" type="float" value="0.500" min="0" max="1" size="5" label="Maximum raw overlap mismatch (0-1)" />
58 <param argument="correctedErrorRate" type="float" value="0.144" min="0" max="1" size="5" label="Maximum corrected overlap mismatch (0-1)" /> 65 <param argument="correctedErrorRate" type="float" value="0.144" min="0" max="1" size="5" label="Maximum corrected overlap mismatch (0-1)" />
59 <param argument="minReadLength" type="integer" value="1000" min="1" size="5" label="Minimum read length" /> 66 <param argument="minReadLength" type="integer" value="1000" min="1" size="5" label="Minimum read length" />
60 <param argument="minOverlapLength" type="integer" value="500" min="1" size="5" label="Minimum overlap" /> 67 <param argument="minOverlapLength" type="integer" value="500" min="1" size="5" label="Minimum overlap" />
61 <param argument="corOutCoverage" type="integer" value="40" min="1" size="5" label="Target coverage for corrected reads" /> 68 <param argument="corOutCoverage" type="integer" value="40" min="1" size="5" label="Target coverage for corrected reads" />
69
70 <section name="contigFilter" title="Contig Filters">
71 <param argument="minReads" type="integer" value="2" min="0" label="Minimum reads" />
72 <param argument="minLength" type="integer" value="0" min="0" label="Minimum length" />
73 <param argument="singleReadSpan" type="float" value="1.0" min="0.0" max="1.0" label="Maximum single read span (fraction)" />
74 <param argument="lowCovSpan" type="float" value="0.5" min="0.0" max="1.0" label="Low coverage span (fraction)" />
75 <param argument="lowCovDepth" type="integer" value="5" min="0" label="Low coverage depth" />
76 </section>
62 77
63 </inputs> 78 </inputs>
64 79
65 <!-- ***************************************************************** --> 80 <!-- ***************************************************************** -->
66 81