Mercurial > repos > bgruening > canu
annotate canu.xml @ 1:58346ef3116b draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
author | bgruening |
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date | Sat, 09 Jun 2018 13:46:56 -0400 |
parents | 4c8f32256fa8 |
children | c5b7390290b1 |
rev | line source |
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0
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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1 <tool id="canu" name="Canu assembler" version="1.7"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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2 <description>Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore </description> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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3 <requirements> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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4 <requirement type="package" version="1.7">canu</requirement> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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5 </requirements> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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6 <version_command>canu --version</version_command> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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7 <command detect_errors="exit_code"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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8 <![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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9 |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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10 #for $counter, $input in enumerate($inputs): |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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11 #if $input.ext in ['fastq.gz', 'fasta.gz'] |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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12 ## linking does not work |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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13 cp '$input' ./input_${counter}.gz && |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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14 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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15 #end for |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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16 |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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17 canu |
1
58346ef3116b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
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18 #if $stage != 'all': |
58346ef3116b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
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19 $stage |
58346ef3116b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
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20 #end if |
0
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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21 -p canu |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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22 -d out_dir |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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23 #if $s: |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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24 -s '$s' |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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25 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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26 genomeSize=$genomeSize |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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27 #if $rawErrorRate: |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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28 rawErrorRate=$rawErrorRate |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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29 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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30 #if $correctedErrorRate: |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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31 correctedErrorRate=$correctedErrorRate |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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32 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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33 minReadLength=$minReadLength |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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34 minOverlapLength=$minOverlapLength |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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35 corOutCoverage=$corOutCoverage |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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36 contigFilter=' |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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37 ${contigFilter.minReads} |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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38 ${contigFilter.minLength} |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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39 ${contigFilter.singleReadSpan} |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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40 ${contigFilter.lowCovSpan} |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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41 ${contigFilter.lowCovDepth} |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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42 ' |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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43 genomeSize=$genomeSize |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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44 stopOnReadQuality=false |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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45 minThreads=\${GALAXY_SLOTS:-4} |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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46 maxThreads=\${GALAXY_SLOTS:-4} |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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47 obtovlThreads=\${GALAXY_SLOTS:-4} |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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48 utgovlThreads=\${GALAXY_SLOTS:-4} |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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49 batThreads=\${GALAXY_SLOTS:-4} |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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50 batMemory=\${GALAXY_MEMORY_MB:-7} |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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51 cormhapMemory=\${GALAXY_MEMORY_MB:-7} |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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52 obtovlMemory=\${GALAXY_MEMORY_MB:-7} |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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53 utgovlMemory=\${GALAXY_MEMORY_MB:-7} |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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54 gfaThreads=\${GALAXY_SLOTS:-4} |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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55 corThreads=\${GALAXY_SLOTS:-4} |
4c8f32256fa8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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56 cnsThreads=\${GALAXY_SLOTS:-4} |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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57 gnuplotTested=true |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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58 useGrid=false |
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59 $mode |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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60 #for $counter, $input in enumerate($inputs): |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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61 #if $input.ext in ['fastq.gz', 'fasta.gz'] |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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62 ./input_${counter}.gz |
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63 #else: |
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64 '$input' |
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65 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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66 #end for |
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67 2>&1 |
1
58346ef3116b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
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68 && |
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69 echo "Check echo" |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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70 ]]> |
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71 </command> |
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72 <inputs> |
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73 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="Input reads" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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74 <param name="mode" type="select" label="Mode"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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75 <option value="-nanopore-raw" selected="true">Nanopore raw</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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76 <option value="-nanopore-corrected">Nanopore corrected</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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77 <option value="-pacbio-raw">PacBio raw</option> |
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78 <option value="-pacbio-corrected">PacBio corrected</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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79 </param> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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80 <param name="stage" type="select" label="To restrict canu to only a specific stage, use"> |
1
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
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81 <option value="all" selected="true">all</option> |
0
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82 <option value="-correct">generate corrected reads</option> |
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83 <option value="-trim">generate trimmed reads</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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84 <option value="-assemble">generate an assembly</option> |
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85 <option value="-trim-assemble">generate trimmed reads and then assemble them</option> |
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86 </param> |
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87 <param argument="genomeSize" type="text" label="Estimated genome size (e.g. 80m, 15k, 2g)"> |
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88 <validator type="empty_field" /> |
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89 </param> |
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90 <param argument="rawErrorRate" type="float" value="" optional="true" min="0" max="1" |
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91 label="Maximum raw overlap mismatch" help="The defaults are 0.300 for PacBio reads and 0.500 for Nanopore reads." /> |
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92 <param argument="correctedErrorRate" type="float" value="" optional="true" min="0" max="1" |
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93 label="Maximum corrected overlap mismatch" help="The allowed difference in an overlap between two corrected reads. Assemblies of |
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94 low coverage or data with biological differences will benefit from a slight increase |
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95 in this. Defaults are 0.045 for PacBio reads and 0.144 for Nanopore reads." /> |
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96 <param argument="minReadLength" type="integer" value="1000" min="1" label="Minimum read length" /> |
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97 <param argument="minOverlapLength" type="integer" value="500" min="1" label="Minimum overlap" /> |
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98 <param argument="corOutCoverage" type="integer" value="40" min="1" label="Target coverage for corrected reads" /> |
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99 <param argument="-s" type="data" format="txt" optional="true" label="Additonal options" help="Additional specifications provided in a canu spec file." /> |
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100 |
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101 <section name="contigFilter" title="Contig Filters"> |
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102 <param argument="minReads" type="integer" value="2" min="0" label="Minimum reads" /> |
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103 <param argument="minLength" type="integer" value="0" min="0" label="Minimum length" /> |
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104 <param argument="singleReadSpan" type="float" value="1.0" min="0.0" max="1.0" label="Maximum single read span (fraction)" /> |
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105 <param argument="lowCovSpan" type="float" value="0.5" min="0.0" max="1.0" label="Low coverage span (fraction)" /> |
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106 <param argument="lowCovDepth" type="integer" value="5" min="0" label="Low coverage depth" /> |
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107 </section> |
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108 </inputs> |
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109 <outputs> |
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110 <data name="contigs" format="fasta" from_work_dir="out_dir/canu.contigs.fasta" label="${tool.name} on ${on_string} (contigs)"> |
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111 <filter>stage == 'all'</filter> |
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112 </data> |
1
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113 <data name="unassembled" format="fasta" from_work_dir="out_dir/canu.unassembled.fasta" label="${tool.name} on ${on_string} (unassembled)"> |
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114 <filter>stage == 'all'</filter> |
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115 </data> |
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116 <data name="unitigs" format="fasta" from_work_dir="out_dir/canu.unitigs.fasta" label="${tool.name} on ${on_string} (unitigs)"> |
1
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117 <filter>stage == 'all'</filter> |
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118 </data> |
1
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119 <data name="corrected_reads" format="fasta.gz" from_work_dir="out_dir/canu.correctedReads.fasta.gz" label="${tool.name} on ${on_string} (corrected reads)"> |
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120 <filter>'-correct' in stage or stage == 'all'</filter> |
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121 </data> |
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122 <data name="trimmed_reads" format="fasta.gz" from_work_dir="out_dir/canu.trimmedReads.fasta.gz" label="${tool.name} on ${on_string} (trimmed reads)"> |
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123 <filter>'-trim' in stage or stage == 'all'</filter> |
0
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124 </data> |
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125 </outputs> |
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126 <tests> |
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127 <test expect_num_outputs="5"> |
0
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128 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/> |
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129 <param name="genomeSize" value="4.6m" /> |
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130 <param name="minReadLength" value="2000" /> |
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131 <output name="contigs" ftype="fasta" file="ecoli_canu_contigs_result1.fa"/> |
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132 <output name="unitigs" ftype="fasta" file="ecoli_canu_unitigs_result1.fa"/> |
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133 <output name="unassembled" ftype="fasta" file="ecoli_canu_unassembled_result1.fa"/> |
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134 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result1.fa.gz"/> |
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135 <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result1.fa.gz"/> |
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136 </test> |
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137 <test expect_num_outputs="5"> |
0
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138 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/> |
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139 <param name="genomeSize" value="4.6m" /> |
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140 <param name="minReadLength" value="2000" /> |
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141 <param name="minOverlapLength" value="800" /> |
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142 <param name="rawErrorRate" value="0.2" /> |
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143 <param name="correctedErrorRate" value="0.05" /> |
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144 <param name="corOutCoverage" value="2" /> |
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145 <output name="contigs" ftype="fasta" file="ecoli_canu_contigs_result2.fa"/> |
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146 <output name="unitigs" ftype="fasta" file="ecoli_canu_unitigs_result2.fa"/> |
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147 <output name="unassembled" ftype="fasta" file="ecoli_canu_unassembled_result2.fa"/> |
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148 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result2.fa.gz"/> |
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149 <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result2.fa.gz"/> |
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150 </test> |
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151 <test expect_num_outputs="1"> |
0
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152 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/> |
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153 <param name="stage" value="-correct"/> |
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154 <param name="minReadLength" value="2500" /> |
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155 <param name="genomeSize" value="4.6m" /> |
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156 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result3.fa.gz"/> |
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157 </test> |
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158 <test expect_num_outputs="1"> |
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159 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/> |
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160 <param name="stage" value="-trim"/> |
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161 <param name="minReadLength" value="2500" /> |
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162 <param name="genomeSize" value="4.6m" /> |
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163 <output name="trimmed_reads" ftype="fasta.gz" compare="sim_size" delta="12000" file="ecoli_canu_trimmed_reads_result4.fa.gz"/> |
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164 </test> |
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165 </tests> |
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166 <help> |
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167 <![CDATA[ |
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168 |
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169 Canu specializes in assembling PacBio or Oxford Nanopore sequences. Canu operates in three phases: correction, trimming and assembly. |
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170 The correction phase will improve the accuracy of bases in reads. The trimming phase will trim reads to the portion that appears to |
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171 be high-quality sequence, removing suspicious regions such as remaining SMRTbell adapter. The assembly phase will order the reads |
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172 into contigs, generate consensus sequences and create graphs of alternate paths. |
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173 |
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174 For eukaryotic genomes, coverage more than 20x is enough to outperform current hybrid methods, however, between 30x and 60x |
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175 coverage is the recommended minimum. More coverage will let Canu use longer reads for assembly, which will result in better assemblies. |
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176 |
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177 http://canu.readthedocs.io |
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178 |
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179 ]]> |
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180 </help> |
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181 <citations> |
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182 <citation type="doi">10.1101/gr.215087.116</citation> |
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183 <citation type="doi">10.1093/bioinformatics/btw753</citation> |
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184 <citation type="doi">10.1038/nbt.3238</citation> |
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185 <citation type="doi">10.1126/science.287.5461.2196</citation> |
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186 <citation type="doi">10.1038/nmeth.4035</citation> |
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187 <citation type="doi">10.1038/nmeth.2474</citation> |
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188 </citations> |
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189 </tool> |