Mercurial > repos > bgruening > canu

annotate canu.xml @ 4:86f150c8019d draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
author bgruening
date Wed, 03 Nov 2021 16:10:37 +0000
parents 5732f959936a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
parents: 2
diff changeset
1 <tool id="canu" name="Canu assembler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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2 <description>Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore</description>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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3 <xrefs>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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4 <xref type="bio.tools">canu</xref>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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5 </xrefs>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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6 <macros>
4
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
bgruening
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7 <token name="@TOOL_VERSION@">2.2</token>
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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8 <token name="@VERSION_SUFFIX@">0</token>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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9 </macros>
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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10 <requirements>
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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11 <requirement type="package" version="@TOOL_VERSION@">canu</requirement>
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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diff changeset
12 </requirements>
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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13 <version_command>canu --version</version_command>
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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14 <command detect_errors="exit_code">
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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15 <![CDATA[
4c8f32256fa8 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
bgruening
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17 #for $counter, $input in enumerate($inputs):
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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18 #if $input.ext in ['fastq.gz', 'fasta.gz']
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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19 ## linking does not work
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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20 cp '$input' ./input_${counter}.gz &&
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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21 #end if
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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22 #end for
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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23
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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24 canu
1
58346ef3116b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
bgruening
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25 #if $stage != 'all':
58346ef3116b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
bgruening
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26 $stage
58346ef3116b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
bgruening
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27 #end if
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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28 -p canu
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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29 -d ./out_dir
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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30 #if $s:
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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31 -s '$s'
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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32 #end if
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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33 #if $rawErrorRate:
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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34 rawErrorRate=$rawErrorRate
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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35 #end if
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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36 #if $correctedErrorRate:
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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diff changeset
37 correctedErrorRate=$correctedErrorRate
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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38 #end if
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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39 minReadLength=$minReadLength
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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40 minOverlapLength=$minOverlapLength
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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41 corOutCoverage=$corOutCoverage
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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42 #if $stopOnLowCoverage
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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43 stopOnLowCoverage=$stopOnLowCoverage
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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44 #end if
4
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
bgruening
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45 #if $minInputCoverage ##and $stage in ["all", "trim-assemble", "assemble"]
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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46 minInputCoverage=$minInputCoverage
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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47 #end if
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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48 contigFilter='
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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49 ${contigFilter.minReads}
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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50 ${contigFilter.minLength}
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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51 ${contigFilter.singleReadSpan}
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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52 ${contigFilter.lowCovSpan}
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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53 ${contigFilter.lowCovDepth}
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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54 '
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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55
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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56 genomeSize='$genomeSize'
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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57 minThreads=\${GALAXY_SLOTS:-4}
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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58 maxThreads=\${GALAXY_SLOTS:-4}
4
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
bgruening
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59 redMemory=\${GALAXY_MEMORY_MB:-6144}M
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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60 redThreads=\${GALAXY_SLOTS:-4}
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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61 obtovlThreads=\${GALAXY_SLOTS:-4}
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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62 utgovlThreads=\${GALAXY_SLOTS:-4}
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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63 batThreads=\${GALAXY_SLOTS:-4}
4
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
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64 batMemory=\${GALAXY_MEMORY_MB:-6144}M
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
bgruening
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65 cormhapMemory=\${GALAXY_MEMORY_MB:-6144}M
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
bgruening
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66 obtovlMemory=\${GALAXY_MEMORY_MB:-6144}M
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
bgruening
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67 utgovlMemory=\${GALAXY_MEMORY_MB:-6144}M
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
bgruening
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68 corThreads=\${GALAXY_SLOTS:-4}
4
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
bgruening
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69 corMemory=\${GALAXY_MEMORY_MB:-6144}M
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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70 cnsThreads=\${GALAXY_SLOTS:-4}
4
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
bgruening
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71 cnsMemory=\${GALAXY_MEMORY_MB:-6144}M
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
bgruening
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72 oeaMemory=\${GALAXY_MEMORY_MB:-6144}M
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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73 oeaThreads=\${GALAXY_SLOTS:-4}
4
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
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74 merylThreads=\${GALAXY_SLOTS:-4}
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
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75 merylMemory=\${GALAXY_MEMORY_MB:-6144}M
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
bgruening
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76 corovlThreads=\${GALAXY_SLOTS:-4}
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
bgruening
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77 corovlMemory=\${GALAXY_MEMORY_MB:-6144}M
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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78 useGrid=false
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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79
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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80 #for $haplotype in $haplotypes:
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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81 -haplotype${haplotype.haplotype_name} '${haplotype.haplotype_input}'
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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82 #end for
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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83
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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84 $technology
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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85 #if $processing:
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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86 $processing
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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87 #end if
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88
0
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89 #for $counter, $input in enumerate($inputs):
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90 #if $input.ext in ['fastq.gz', 'fasta.gz']
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91 ./input_${counter}.gz
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92 #else:
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93 '$input'
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94 #end if
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95 #end for
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96 2>&1
3
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97
0
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98 ]]>
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99 </command>
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100 <inputs>
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101 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="Input reads"/>
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102 <repeat name="haplotypes" min="0" max="2" title="Haplotypes for Trio Binning Assembly" help="Canu has support for using parental short-read sequencing to classify and bin">
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103 <param name="haplotype_input" type="data" format="fasta,fastq" multiple="true" label="Haplotype input reads"/>
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104 <param name="haplotype_name" type="text" label="Shot name to identify your haplotype"/>
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105 </repeat>
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106 <param name="technology" type="select" label="Technology">
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107 <option value="-nanopore" selected="true">Nanopore</option>
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108 <option value="-pacbio">PacBio</option>
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109 <option value="-pacbio-hifi">PacBio HiFi</option>
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110 </param>
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111 <param name="processing" type="select" optional="true" label="Processing">
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112 <option value="-corrected">Corrected</option>
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113 <option value="-trimmed">Trimmed</option>
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114 </param>
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115 <param name="stage" type="select" label="To restrict canu to only a specific stage, use">
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116 <option value="all" selected="true">all</option>
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117 <option value="-haplotype">generate haplotype-specific reads</option>
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118 <option value="-correct">generate corrected reads</option>
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119 <option value="-trim">generate trimmed reads</option>
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120 <option value="-assemble">generate an assembly</option>
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121 <option value="-trim-assemble">generate trimmed reads and then assemble them</option>
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122 </param>
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123 <param argument="genomeSize" type="text" label="Estimated genome size (e.g. 8.0m, 15k, 2g)">
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124 <validator type="empty_field"/>
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125 <validator type="expression" message="Only values similar to 8.0m, 15k or 2g are allowed.">value.replace('.', '').isalnum() and value[-1] in ['m', 'k', 'g'] and float(value[:-1])</validator>
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126 </param>
3
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127 <param argument="rawErrorRate" type="float" value="" optional="true" min="0" max="1" label="Maximum raw overlap mismatch" help="The defaults are 0.300 for PacBio reads and 0.500 for Nanopore reads."/>
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128 <param argument="correctedErrorRate" type="float" value="" optional="true" min="0" max="1" label="Maximum corrected overlap mismatch" help="The allowed difference in an overlap between two corrected reads. Assemblies of low coverage or data with biological differences will benefit from a slight increase in this. Defaults are 0.045 for PacBio reads and 0.144 for Nanopore reads."/>
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129 <param argument="minReadLength" type="integer" value="1000" min="1" label="Minimum read length"/>
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130 <param argument="minOverlapLength" type="integer" value="500" min="1" label="Minimum overlap"/>
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131 <param argument="minInputCoverage" type="integer" value="" min="1" optional="true" label="Minimum Input Coverage"/>
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132 <param argument="corOutCoverage" type="integer" value="40" min="1" label="Target coverage for corrected reads"/>
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133 <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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134 <param argument="stopOnLowCoverage" type="integer" value="10" min="1" label="Stop the assembly if read coverage is too low to be useful" help="Coverage is checked whene when input sequences are initially loaded into the sequence store, when corrected reads are generated, and when read ends are trimmed off."/>
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135 <section name="contigFilter" title="Contig Filters">
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136 <param argument="minReads" type="integer" value="2" min="0" label="Minimum reads"/>
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137 <param argument="minLength" type="integer" value="0" min="0" label="Minimum length"/>
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138 <param argument="singleReadSpan" type="float" value="1.0" min="0.0" max="1.0" label="Maximum single read span (fraction)"/>
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139 <param argument="lowCovSpan" type="float" value="0.5" min="0.0" max="1.0" label="Low coverage span (fraction)"/>
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140 <param argument="lowCovDepth" type="integer" value="5" min="0" label="Low coverage depth"/>
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141 </section>
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142 </inputs>
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143 <outputs>
3
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144 <data name="report" format="txt" from_work_dir="out_dir/canu.report" label="${tool.name} on ${on_string} (report)"/>
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145 <data name="contigs" format="fasta" from_work_dir="out_dir/canu.contigs.fasta" label="${tool.name} on ${on_string} (contigs)">
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146 <filter>stage == 'all'</filter>
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147 </data>
1
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148 <data name="unassembled" format="fasta" from_work_dir="out_dir/canu.unassembled.fasta" label="${tool.name} on ${on_string} (unassembled)">
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149 <filter>stage == 'all'</filter>
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150 </data>
1
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151 <data name="corrected_reads" format="fasta.gz" from_work_dir="out_dir/canu.correctedReads.fasta.gz" label="${tool.name} on ${on_string} (corrected reads)">
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152 <filter>'-correct' in stage or stage == 'all'</filter>
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153 </data>
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154 <data name="trimmed_reads" format="fasta.gz" from_work_dir="out_dir/canu.trimmedReads.fasta.gz" label="${tool.name} on ${on_string} (trimmed reads)">
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155 <filter>'-trim' in stage or stage == 'all'</filter>
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156 </data>
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157 </outputs>
3
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158 <tests>
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159 <test expect_num_outputs="5">
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160 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/>
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161 <param name="technology" value="-nanopore"/>
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162 <param name="genomeSize" value="20k"/>
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163 <param name="stopOnLowCoverage" value="1"/>
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164 <param name="minInputCoverage" value="1"/>
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165 <param name="minReadLength" value="2000"/>
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166 <output name="contigs" ftype="fasta" file="ecoli_canu_contigs_result1.fa"/>
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167 <output name="unassembled" ftype="fasta" file="ecoli_canu_unassembled_result1.fa"/>
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168 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result1.fa.gz"/>
58346ef3116b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
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169 <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result1.fa.gz"/>
3
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170 <output name="report">
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171 <assert_contents>
4
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172 <has_n_lines n="486"/>
3
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173 <has_text_matching expression="[UNITIGGING/CONTIGS]"/>
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174 <has_text_matching expression="-- Contig sizes based on genome size 20kbp:"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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175 </assert_contents>
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176 </output>
0
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177 </test>
1
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178 <test expect_num_outputs="5">
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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179 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/>
3
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180 <param name="technology" value="-nanopore"/>
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181 <param name="genomeSize" value="20k"/>
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182 <param name="stopOnLowCoverage" value="1"/>
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183 <param name="minInputCoverage" value="1"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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184 <param name="minReadLength" value="2000"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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185 <param name="minOverlapLength" value="800"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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186 <param name="rawErrorRate" value="0.2"/>
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187 <param name="correctedErrorRate" value="0.05"/>
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188 <param name="corOutCoverage" value="2"/>
1
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189 <output name="contigs" ftype="fasta" file="ecoli_canu_contigs_result2.fa"/>
58346ef3116b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
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190 <output name="unassembled" ftype="fasta" file="ecoli_canu_unassembled_result2.fa"/>
58346ef3116b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
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191 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result2.fa.gz"/>
58346ef3116b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
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192 <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result2.fa.gz"/>
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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193 <output name="report">
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194 <assert_contents>
4
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195 <has_n_lines n="456"/>
3
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196 <has_text_matching expression="[UNITIGGING/CONTIGS]"/>
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197 <has_text_matching expression="-- Contig sizes based on genome size 20kbp:"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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198 </assert_contents>
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199 </output>
0
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200 </test>
3
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201 <test expect_num_outputs="2">
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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202 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/>
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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203 <param name="technology" value="-nanopore"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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204 <param name="genomeSize" value="20k"/>
0
4c8f32256fa8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit b7904bf39167833b3d3648e250726615f75f7525
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205 <param name="stage" value="-correct"/>
3
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bgruening
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206 <param name="stopOnLowCoverage" value="1"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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207 <param name="minReadLength" value="2500"/>
1
58346ef3116b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
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parents: 0
diff changeset
208 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result3.fa.gz"/>
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
bgruening
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209 <output name="report">
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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210 <assert_contents>
4
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211 <has_n_lines n="189"/>
3
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212 <has_text_matching expression="[TRIMMING/READS]"/>
4
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213 <has_text_matching expression="-- Found 93 reads."/>
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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214 </assert_contents>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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215 </output>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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216 </test>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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217 <!--trimming test - it does currently not trim anything due to the input data -->
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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218 <test expect_num_outputs="2">
1
58346ef3116b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
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parents: 0
diff changeset
219 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/>
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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220 <param name="technology" value="-nanopore"/>
4
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
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diff changeset
221 <param name="processing" value="-corrected"/>
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
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222 <!-- <param name="minInputCoverage" value="1"/> -->
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
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223 <param name="genomeSize" value="0.01m"/>
1
58346ef3116b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
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parents: 0
diff changeset
224 <param name="stage" value="-trim"/>
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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225 <param name="minReadLength" value="500"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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226 <output name="report">
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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227 <assert_contents>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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228 <has_text_matching expression="[TRIMMING/READS]"/>
4
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
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229 <has_n_lines n="209"/>
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
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230 <has_text_matching expression="Found 112 reads."/><!-- before trimming -->
86f150c8019d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
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231 <has_text_matching expression="Found 61 reads."/><!-- after trimming -->
3
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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232 </assert_contents>
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233 </output>
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234 </test>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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235 <!--test expect_num_outputs="5">
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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236 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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237 <param name="technology" value="-pacbio"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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238 <repeat name="haplotypes">
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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239 <param name="haplotype_name" value="K12"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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240 <param name="haplotype_input" ftype="fasta" value="ecoli-reads.fasta"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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241 </repeat>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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242 <repeat name="haplotypes">
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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diff changeset
243 <param name="haplotype_name" value="K13"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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244 <param name="haplotype_input" ftype="fasta" value="ecoli-reads.fasta"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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245 </repeat>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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246 <param name="genomeSize" value="20k"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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247 <param name="stopOnLowCoverage" value="1"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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248 <param name="minInputCoverage" value="1"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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249 <param name="minReadLength" value="2000"/>
5732f959936a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 7000c7eb839b77a0e7e91874048219bd3a3f5d47"
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250 <output name="contigs" ftype="fasta" file="ecoli_canu_contigs_result5.fa"/>
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251 <output name="unassembled" ftype="fasta" file="ecoli_canu_unassembled_result5.fa"/>
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252 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result5.fa.gz"/>
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253 <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result5.fa.gz"/>
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254 </test-->
0
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255 </tests>
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256 <help>
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257 <![CDATA[
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258
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259 Canu specializes in assembling PacBio or Oxford Nanopore sequences. Canu operates in three phases: correction, trimming and assembly.
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260 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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261 be high-quality sequence, removing suspicious regions such as remaining SMRTbell adapter. The assembly phase will order the reads
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262 into contigs, generate consensus sequences and create graphs of alternate paths.
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263
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264 For eukaryotic genomes, coverage more than 20x is enough to outperform current hybrid methods, however, between 30x and 60x
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265 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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266
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267 http://canu.readthedocs.io
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268
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269 ]]>
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270 </help>
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271 <citations>
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272 <citation type="doi">10.1101/gr.215087.116</citation>
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273 <citation type="doi">10.1093/bioinformatics/btw753</citation>
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274 <citation type="doi">10.1038/nbt.3238</citation>
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275 <citation type="doi">10.1126/science.287.5461.2196</citation>
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276 <citation type="doi">10.1038/nmeth.4035</citation>
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277 <citation type="doi">10.1038/nmeth.2474</citation>
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278 </citations>
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279 </tool>