Mercurial > repos > bgruening > flye
annotate flye.xml @ 11:291923e6f276 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
author | bgruening |
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date | Mon, 18 Mar 2024 12:44:09 +0000 |
parents | cb8dfd28c16f |
children | 3e4f8642c77e |
rev | line source |
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8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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1 <tool id="flye" name="Flye" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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2 <description>de novo assembler for single molecule sequencing reads</description> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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3 <macros> |
d9f4c141d88a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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4 <import>macros.xml</import> |
d9f4c141d88a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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5 </macros> |
11
291923e6f276
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
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6 <expand macro="edam_ontology"/> |
291923e6f276
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
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7 <expand macro="xrefs"/> |
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d9f4c141d88a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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8 <expand macro="requirements" /> |
d9f4c141d88a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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9 <version_command>flye --version</version_command> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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10 <command detect_errors="exit_code"><![CDATA[ |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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11 #for $counter, $input in enumerate($inputs): |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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12 #if $input.is_of_type('fastqsanger', 'fastq'): |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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13 #set $ext = 'fastq' |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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14 #elif $input.is_of_type('fastqsanger.gz', 'fastq.gz'): |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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15 #set $ext = 'fastq.gz' |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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16 #elif $input.is_of_type('fasta.gz'): |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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17 #set $ext = 'fasta.gz' |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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18 #elif $input.is_of_type('fasta'): |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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19 #set $ext = 'fasta' |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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20 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
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21 ln -sf '$input' ./input_${counter}.${ext} && |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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22 #end for |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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23 flye |
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24 $mode_conditional.mode |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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25 #for $counter, $input in enumerate($inputs): |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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26 ./input_${counter}.$ext |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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27 #end for |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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28 -o out_dir |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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29 -t \${GALAXY_SLOTS:-4} |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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30 -i $iterations |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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31 #if $mode_conditional.mode == '--pacbio-hifi' and $mode_conditional.hifi_error: |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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32 --hifi-error $mode_conditional.hifi_error |
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33 #end if |
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34 #if $min_overlap: |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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35 -m $min_overlap |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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36 #end if |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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37 #if $asm.asm_select == 'true': |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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38 --asm-coverage $asm.asm_coverage |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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39 -g '${asm.genome_size}' |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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40 #end if |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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41 $meta |
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42 $scaffold |
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43 $no_alt_contigs |
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d9f4c141d88a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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44 ]]></command> |
d9f4c141d88a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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45 <inputs> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 6cd5f829f985631f0e8360d66a73206389101171
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46 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" /> |
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276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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47 <conditional name="mode_conditional"> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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48 <param name="mode" type="select" label="Mode"> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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49 <option value="--nano-raw">Nanopore raw (--nano-raw)</option> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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50 <option value="--nano-corr">Nanopore corrected (--nano-corr)</option> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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51 <option value="--nano-hq">Nanopore HQ (--nano-hq)</option> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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52 <option value="--pacbio-raw">PacBio raw (--pacbio-raw)</option> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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53 <option value="--pacbio-corr">PacBio corrected (--pacbio-corr)</option> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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54 <option value="--pacbio-hifi">PacBio HiFi (--pacbio-hifi)</option> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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55 </param> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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56 <when value="--nano-raw"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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57 <when value="--nano-corr"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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58 <when value="--nano-hq"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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59 <when value="--pacbio-raw"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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60 <when value="--pacbio-corr"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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61 <when value="--pacbio-hifi"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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62 <param argument="--hifi-error" type="float" min="0" max="1" optional="true" label="Expected HiFi reads error rate" help="Default: 0.01"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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63 </when> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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64 </conditional> |
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65 <param argument="--iterations" type="integer" value="1" label="Number of polishing iterations" |
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66 help="Polishing is performed as the final assembly stage. By default, Flye runs one polishing iteration. Additional iterations |
e27815e82dd4
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67 might correct a small number of extra errors (due to improvements on how reads may align to the corrected assembly). If the |
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68 parameter is set to 0, the polishing is not performed"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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69 <param argument="--min-overlap" type="integer" min="1000" max="10000" optional="true" label="Minimum overlap between reads" |
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70 help="This sets a minimum overlap length for two reads to be considered overlapping. By default it is chosen |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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71 automatically based on the read length distribution (reads N90) and does not require manual setting. Typical |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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72 value is 3k-5k (and down to 1k for datasets with shorter read length). Intuitively, we want to set this |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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73 parameter as high as possible, so the repeat graph is less tangled. However, higher values might lead to assembly gaps. |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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74 In some rare cases it makes sense to manually increase minimum overlap for assemblies of big genomes with long reads and high coverage." /> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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75 <param argument="--keep-haplotypes" type="boolean" truevalue="--keep-haplotypes" falsevalue="" checked="False" label="Keep haplotypes" |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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76 help="By default, Flye collapses graph structures caused by alternative haplotypes (bubbles, superbubbles, roundabouts) to produce longer |
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77 consensus contigs. This option retains the alternative paths on the graph, producing less contigouos, but more detailed assembly."/> |
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78 <param argument="--scaffold" type="boolean" truevalue="--scaffold" falsevalue="" label="Enable scaffolding using graph" |
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79 help="Starting from the version 2.9 Flye does not perform scaffolding by default, which guarantees that all assembled sequences do not have any gaps" /> |
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80 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="Perform metagenomic assembly" |
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81 help="It is designed for highly non-uniform coverage and is sensitive to underrepresented sequence at low coverage (as low as 2x). |
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82 In some examples of simple metagenomes, we observed that the normal mode assembled more contigious bacterial |
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83 consensus sequence, while the metagenome mode was slightly more fragmented, but revealed strain mixtures"/> |
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84 <conditional name="asm"> |
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85 <param name="asm_select" type="select" label="Reduced contig assembly coverage" help="Typically, assemblies of large genomes at high coverage require a hundreds of RAM. For high coverage assemblies, |
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86 you can reduce memory usage by using only a subset of longest reads for initial contig extension stage (usually, the memory bottleneck)"> |
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87 <option value="true">Enable reduced coverage for initial disjointing assembly</option> |
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88 <option value="false" selected="true">Disable reduced coverage for initial disjointing assembly</option> |
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89 </param> |
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90 <when value="true"> |
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91 <param argument="--asm-coverage" type="integer" min="0" value="30" |
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92 label="Reduced coverage for initial disjointing assembly" |
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93 help="This parameter specifies the target coverage of the longest reads. For a typical assembly, 30x is enough to produce good |
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94 initial contigs. Regardless of this parameter, all reads will be used at the later pipeline stages."/> |
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95 <param argument="--genome-size" type="text" optional="true" label="Estimated genome size" |
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96 help="For example, 5m or 2.6g. No longer required as input. However, it must be used in conjunction with --asm-coverage option."> |
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97 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator> |
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98 </param> |
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99 </when> |
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100 <when value="false" /> |
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101 </conditional> |
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102 <param argument="--no-alt-contigs" type="boolean" truevalue="--no-alt-contigs" falsevalue="" checked="false" label="Remove all non-primary contigs from the assembly"/> |
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103 <param name="generate_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a log file"/> |
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104 </inputs> |
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105 <outputs> |
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106 <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/> |
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107 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/> |
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108 <data name="assembly_gfa" format="txt" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/> |
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109 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string}: assembly info"/> |
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110 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string}: log"> |
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111 <filter>generate_log</filter> |
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112 </data> |
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113 </outputs> |
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114 <tests> |
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115 <!--Test 01: pacbio-raw--> |
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116 <test expect_num_outputs="5"> |
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117 <param name="inputs" ftype="fastq.gz" value="ecoli_01.fastq.gz,ecoli_02.fastq.gz,ecoli_03.fastq.gz,ecoli_04.fastq.gz,ecoli_05.fastq.gz,ecoli_06.fastq.gz,ecoli_07.fastq.gz"/> |
0
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118 <param name="mode" value="--pacbio-raw"/> |
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119 <param name="iterations" value="0"/> |
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120 <param name="generate_log" value="true"/> |
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121 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/> |
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122 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> |
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123 <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="txt" compare="sim_size"/> |
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124 <output name="consensus" file="result1_assembly.fasta" ftype="fasta" compare="sim_size"/> |
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125 <output name="flye_log" file="result1.log" ftype="txt" compare="sim_size"/> |
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126 </test> |
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127 <!--Test 02: nano raw--> |
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128 <test expect_num_outputs="4"> |
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129 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/> |
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130 <param name="mode" value="--nano-raw"/> |
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131 <param name="iterations" value="0"/> |
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132 <output name="assembly_info" ftype="tabular"> |
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133 <assert_contents> |
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134 <has_size value="95" delta="100"/> |
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135 </assert_contents> |
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136 </output> |
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137 <output name="assembly_graph" ftype="graph_dot"> |
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138 <assert_contents> |
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139 <has_size value="803" delta="100"/> |
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140 </assert_contents> |
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141 </output> |
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142 <output name="assembly_gfa" ftype="txt"> |
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143 <assert_contents> |
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144 <has_size value="35047" delta="100"/> |
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145 </assert_contents> |
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146 </output> |
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147 <output name="consensus" ftype="fasta"> |
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148 <assert_contents> |
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149 <has_size value="35573" delta="100"/> |
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150 </assert_contents> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
151 </output> |
4
3ee0ef312022
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
bgruening
parents:
3
diff
changeset
|
152 </test> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
153 <!--Test 03: reduce coverage--> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
154 <test expect_num_outputs="4"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
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|
155 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
156 <conditional name="mode_conditional"> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
157 <param name="mode" value="--nano-raw"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
158 </conditional> |
6
0284be52bfcf
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents:
5
diff
changeset
|
159 <conditional name="asm"> |
0284be52bfcf
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents:
5
diff
changeset
|
160 <param name="asm_select" value="true" /> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
161 <param name="asm" value="30"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
162 <param name="genome_size" value="3980000"/> |
6
0284be52bfcf
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents:
5
diff
changeset
|
163 </conditional> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
164 <output name="assembly_info" ftype="tabular"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
165 <assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
166 <has_size value="286" delta="100"/> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
167 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
168 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
169 <output name="assembly_graph" ftype="graph_dot"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
170 <assert_contents> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
171 <has_size value="1840" delta="100"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
172 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
173 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
174 <output name="assembly_gfa" ftype="txt"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
175 <assert_contents> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
176 <has_size value="420752" delta="100"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
177 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
178 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
179 <output name="consensus" ftype="fasta"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
180 <assert_contents> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
181 <has_size value="427580" delta="100"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
182 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
183 </output> |
0
d9f4c141d88a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff
changeset
|
184 </test> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
185 <!--Test 04: metagenomic mode--> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
186 <test expect_num_outputs="4"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
187 <param name="inputs" ftype="fastq.gz" value="ecoli_01.fastq.gz,ecoli_02.fastq.gz,ecoli_03.fastq.gz,ecoli_04.fastq.gz,ecoli_05.fastq.gz,ecoli_06.fastq.gz,ecoli_07.fastq.gz"/> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
188 <conditional name="mode_conditional"> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
189 <param name="mode" value="--pacbio-raw"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
190 </conditional> |
4
3ee0ef312022
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
bgruening
parents:
3
diff
changeset
|
191 <param name="meta" value="true"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
192 <output name="assembly_info" ftype="tabular"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
193 <assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
194 <has_size value="95" delta="100"/> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
195 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
196 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
197 <output name="assembly_graph" ftype="graph_dot"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
198 <assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
199 <has_size value="367" delta="100"/> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
200 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
201 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
202 <output name="assembly_gfa" ftype="txt"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
203 <assert_contents> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
204 <has_size value="418729" delta="100"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
205 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
206 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
207 <output name="consensus" ftype="fasta"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
208 <assert_contents> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
209 <has_size value="425667" delta="100"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
210 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
211 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
212 </test> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
213 <!--Test 05: nanopore HQ mode--> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
214 <test expect_num_outputs="4"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
215 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
216 <conditional name="mode_conditional"> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
217 <param name="mode" value="--nano-hq"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
218 </conditional> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
219 <param name="min_overlap" value="1000"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
220 <output name="assembly_info" ftype="tabular"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
221 <assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
222 <has_size value="286" delta="100"/> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
223 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
224 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
225 <output name="assembly_graph" ftype="graph_dot"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
226 <assert_contents> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
8
diff
changeset
|
227 <has_size value="1248" delta="100"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
diff
changeset
|
228 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
7
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229 </output> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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230 <output name="assembly_gfa" ftype="txt"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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231 <assert_contents> |
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232 <has_size value="419414" delta="100"/> |
8
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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233 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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234 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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235 <output name="consensus" ftype="fasta"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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236 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
bgruening
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237 <has_size value="426277" delta="100"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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238 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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239 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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240 </test> |
9
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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241 <!--Test 06: hifi error option--> |
8
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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242 <test expect_num_outputs="4"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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243 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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244 <conditional name="mode_conditional"> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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245 <param name="mode" value="--pacbio-hifi"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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246 <param name="hifi_error" value="0.21"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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247 </conditional> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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248 <param name="min_overlap" value="1000"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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249 <output name="assembly_info" ftype="tabular"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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250 <assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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251 <has_size value="286" delta="100"/> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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252 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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253 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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254 <output name="assembly_graph" ftype="graph_dot"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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255 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
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256 <has_size value="1500" delta="100"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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257 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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258 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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259 <output name="assembly_gfa" ftype="txt"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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260 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
bgruening
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261 <has_size value="418422" delta="100"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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262 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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263 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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264 <output name="consensus" ftype="fasta"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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265 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
bgruening
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266 <has_size value="425147" delta="200"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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267 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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268 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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269 </test> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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270 <!--Test 07: keep haplotypes--> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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271 <test expect_num_outputs="4"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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272 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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273 <conditional name="mode_conditional"> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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274 <param name="mode" value="--pacbio-corr"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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275 <param name="hifi_error" value="0.21"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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276 </conditional> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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277 <param name="min_overlap" value="1000"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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278 <param name="keep-haplotypes" value="true"/> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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279 <output name="assembly_info" ftype="tabular"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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280 <assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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281 <has_size value="286" delta="100"/> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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282 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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283 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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284 <output name="assembly_graph" ftype="graph_dot"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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285 <assert_contents> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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286 <has_size value="1273" delta="100"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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287 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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288 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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289 <output name="assembly_gfa" ftype="txt"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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290 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
bgruening
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291 <has_size value="418511" delta="100"/> |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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292 </assert_contents> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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293 </output> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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|
294 <output name="consensus" ftype="fasta"> |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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295 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
bgruening
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296 <has_size value="425267" delta="100"/> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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297 </assert_contents> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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298 </output> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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299 </test> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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|
300 <!--Test 08: scaffolding mode--> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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301 <test expect_num_outputs="4"> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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|
302 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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303 <param name="mode" value="--nano-hq"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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304 <param name="min_overlap" value="1000"/> |
11
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
bgruening
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|
305 <param name="scaffold" value="true"/> |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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|
306 <output name="assembly_info" ftype="tabular"> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents:
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diff
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|
307 <assert_contents> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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308 <has_size value="286" delta="100"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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309 </assert_contents> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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310 </output> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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311 <output name="assembly_graph" ftype="graph_dot"> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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312 <assert_contents> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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313 <has_size value="1248" delta="100"/> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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314 </assert_contents> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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315 </output> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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316 <output name="assembly_gfa" ftype="txt"> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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317 <assert_contents> |
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318 <has_size value="419414" delta="1000"/> |
9
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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319 </assert_contents> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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320 </output> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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321 <output name="consensus" ftype="fasta"> |
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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322 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
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323 <has_size value="426277" delta="1000"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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324 </assert_contents> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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325 </output> |
0
d9f4c141d88a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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326 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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327 <!--Test 09: test not-alt-contigs parameter w--> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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328 <test expect_num_outputs="4"> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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329 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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330 <param name="mode" value="--nano-raw"/> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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331 <param name="iterations" value="0"/> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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332 <param name="no_alt_contigs" value="true"/> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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333 <output name="assembly_info" ftype="tabular"> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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334 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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335 <has_size value="151" delta="100"/> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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336 </assert_contents> |
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337 </output> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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338 <output name="assembly_graph" ftype="graph_dot"> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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339 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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340 <has_size value="217" delta="100"/> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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341 </assert_contents> |
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342 </output> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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343 <output name="assembly_gfa" ftype="txt"> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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344 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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345 <has_size value="5110" delta="100"/> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
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346 </assert_contents> |
cb8dfd28c16f
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347 </output> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
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348 <output name="consensus" ftype="fasta"> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
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349 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
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350 <has_size value="5123" delta="100"/> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
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351 </assert_contents> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
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352 </output> |
cb8dfd28c16f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
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353 </test> |
0
d9f4c141d88a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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354 </tests> |
d9f4c141d88a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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355 <help><![CDATA[ |
d9f4c141d88a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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356 |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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357 **Purpose** |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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358 |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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359 Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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360 It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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361 a complete pipeline: it takes raw PacBio/ONT reads as input and outputs polished contigs. Flye also has a special mode for metagenome |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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362 assembly. |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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363 |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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364 ---- |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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365 |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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|
366 **Quick usage** |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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367 |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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368 Input reads can be in FASTA or FASTQ format, uncompressed or compressed with gz. Currently, PacBio (raw, corrected, HiFi) and ONT reads |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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369 (raw, corrected) are supported. Expected error rates are <30% for raw, <3% for corrected, and <1% for HiFi. Note that Flye was primarily |
9
276f5d8712d5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
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370 developed to run on raw reads. You may specify multiple files with reads (separated by spaces). Mixing different read types is not yet supported. The *--meta* o |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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371 ption enables the mode for metagenome/uneven coverage assembly. |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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372 |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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373 Genome size estimate is no longer a required option. You need to provide an estimate if using *--asm-coverage* option. |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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|
374 |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents:
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375 To reduce memory consumption for large genome assemblies, you can use a subset of the longest reads for initial disjointig assembly by |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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|
376 specifying *--asm-coverage* and *--genome-size* options. Typically, 40x coverage is enough to produce good disjointigs. |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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|
377 |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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|
378 ---- |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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|
379 |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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|
380 **Outputs** |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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|
381 |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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382 The main output files are: |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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|
383 |
11
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
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|
384 * Final assembly: contains contigs and possibly scaffolds (see below). |
291923e6f276
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
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385 * Final repeat graph: note that the edge sequences might be different (shorter) than contig sequences, because contigs might include multiple graph edges. |
291923e6f276
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
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386 * Extra information about contigs (such as length or coverage). |
8
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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|
387 |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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388 Each contig is formed by a single unique graph edge. If possible, unique contigs are extended with the sequence from flanking unresolved repeats on the graph. Thus, |
e27815e82dd4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
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389 a contig fully contains the corresponding graph edge (with the same id), but might be longer then this edge. This is somewhat similar to unitig-contig relation in |
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390 OLC assemblers. In a rare case when a repetitive graph edge is not covered by the set of "extended" contigs, it will be also output in the assembly file. |
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391 |
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392 Sometimes it is possible to further order contigs into scaffolds based on the repeat graph structure. These ordered contigs will be output as a part of scaffold in |
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393 the assembly file (with a scaffold prefix). Since it is hard to give a reliable estimate of the gap size, those gaps are represented with the default 100 Ns. |
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394 assembly_info.txt file (below) contains additional information about how scaffolds were formed. |
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395 |
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396 Extra information about contigs/scaffolds is output into the assembly_info.txt file. It is a tab-delimited table with the columns as follows: |
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397 |
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398 * Contig/scaffold id |
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399 * Length |
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400 * Coverage |
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401 * Is circular, (Y)es or (N)o |
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402 * Is repetitive, (Y)es or (N)o |
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403 * Multiplicity (based on coverage) |
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404 * Alternative group |
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405 * Graph path (graph path corresponding to this contig/scaffold). |
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406 |
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407 Scaffold gaps are marked with `??` symbols, and `*` symbol denotes a terminal graph node. Alternative contigs (representing alternative haplotypes) will have the same alt. |
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408 group ID. Primary contigs are marked by `*`. |
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409 |
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410 ---- |
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411 |
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412 **Algorithm Description** |
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413 |
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414 This is a brief description of the Flye algorithm. Please refer to the manuscript for more detailed information. The draft contig extension is organized as follows: |
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415 |
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416 * K-mer counting / erroneous k-mer pre-filtering |
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417 * Solid k-mer selection (k-mers with sufficient frequency, which are unlikely to be erroneous) |
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418 * Contig extension. The algorithm starts from a single read and extends it with a next overlapping read (overlaps are dynamically detected using the selected solid k-mers). |
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419 |
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420 Note that we do not attempt to resolve repeats at this stage, thus the reconstructed contigs might contain misassemblies. Flye then aligns the reads on these draft |
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421 contigs using minimap2 and calls a consensus. Afterwards, Flye performs repeat analysis as follows: |
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422 |
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423 * Repeat graph is constructed from the (possibly misassembled) contigs |
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424 * In this graph all repeats longer than minimum overlap are collapsed |
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425 * The algorithm resolves repeats using the read information and graph structure |
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426 * The unbranching paths in the graph are output as contigs |
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427 |
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428 If enabled, after resolving bridged repeats, Trestle module attempts to resolve simple unbridged repeats (of multiplicity 2) using the heterogeneities between repeat copies. |
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429 Finally, Flye performs polishing of the resulting assembly to correct the remaining errors: |
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430 |
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431 * Alignment of all reads to the current assembly using minimap2 |
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432 * Partition the alignment into mini-alignments (bubbles) |
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433 * Error correction of each bubble using a maximum likelihood approach |
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434 |
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435 The polishing steps could be repeated, which might slightly increase quality for some datasets. |
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436 |
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437 |
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438 ]]></help> |
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439 <expand macro="citations" /> |
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440 </tool> |