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comparison canu.xml @ 1:ed5df116fad3 draft

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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 21:40:46 -0400
parents 7d87a6450883
children a5198537f8a2
comparison
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0:7d87a6450883 1:ed5df116fad3
23 canu 23 canu
24 24
25 -p canu_galaxy 25 -p canu_galaxy
26 -d out_dir 26 -d out_dir
27 useGrid=false 27 useGrid=false
28 genomeSize=$genome_size 28 genomeSize=$genomeSize
29 rawErrorRate=$raw_error_rate 29 rawErrorRate=$rawErrorRate
30 correctedErrorRate=$corrected_error_rate 30 correctedErrorRate=$correctedErrorRate
31 minReadLength=$min_read_length 31 minReadLength=$minReadLength
32 minOverlapLength=$min_overlap 32 minOverlapLength=$minOverlapLength
33 corOutCoverage=$corOutCoverage
33 minThreads=\${GALAXY_SLOTS:-1} 34 minThreads=\${GALAXY_SLOTS:-1}
34 maxThreads=\${GALAXY_SLOTS:-1} 35 maxThreads=\${GALAXY_SLOTS:-1}
35 gnuplotTested=true 36 gnuplotTested=true
36 useGrid=false 37 useGrid=false
37 $mode 38 $mode
50 <option value="-nanopore-raw" selected="true">nanopore raw</option> 51 <option value="-nanopore-raw" selected="true">nanopore raw</option>
51 <option value="-pacbio-raw">pacbio raw</option> 52 <option value="-pacbio-raw">pacbio raw</option>
52 <option value="-nanopore-corrected">nanopore corrected</option> 53 <option value="-nanopore-corrected">nanopore corrected</option>
53 <option value="-pacbio-corrected">pacbio corrected</option> 54 <option value="-pacbio-corrected">pacbio corrected</option>
54 </param> 55 </param>
55 <param name="genome_size" type="text" size="5" label="Estimated genome size (e.g. 80m, 15k, 2g)" /> 56 <param argument="genomeSize" type="text" size="5" label="Estimated genome size (e.g. 80m, 15k, 2g)" />
56 <param name="raw_error_rate" type="float" value="0.500" min="0" max="1" size="5" label="Maximum raw overlap mismatch (0-1)" /> 57 <param argument="rawErrorRate" type="float" value="0.500" min="0" max="1" size="5" label="Maximum raw overlap mismatch (0-1)" />
57 <param name="corrected_error_rate" type="float" value="0.144" min="0" max="1" size="5" label="Maximum corrected 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)" />
58 <param name="min_read_length" type="integer" value="1000" min="1" size="5" label="Minimum read length" /> 59 <param argument="minReadLength" type="integer" value="1000" min="1" size="5" label="Minimum read length" />
59 <param name="min_overlap" type="integer" value="500" min="1" size="5" label="Minimum overlap" /> 60 <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" />
60 62
61 </inputs> 63 </inputs>
62 64
63 <!-- ***************************************************************** --> 65 <!-- ***************************************************************** -->
64 66
69 71
70 </outputs> 72 </outputs>
71 73
72 <!-- ***************************************************************** --> 74 <!-- ***************************************************************** -->
73 75
74 <!--
75 <tests> 76 <tests>
76 <test>
77 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" />
78 <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
79 </test>
80 </tests> 77 </tests>
81 -->
82 78
83 <!-- ***************************************************************** --> 79 <!-- ***************************************************************** -->
84 80
85 <help> 81 <help>
86 <![CDATA[ 82 <![CDATA[