Mercurial > repos > iuc > quast
annotate quast.xml @ 9:481a230d9f1d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
|---|---|
| date | Wed, 01 Sep 2021 08:18:25 +0000 |
| parents | 4c2bef52f68e |
| children | e377f054bcd0 |
| rev | line source |
|---|---|
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4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
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changeset
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1 <tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy1" profile="18.01"> |
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0
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
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changeset
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2 <description>Genome assembly Quality</description> |
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9
481a230d9f1d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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3 <xrefs> |
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481a230d9f1d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
8
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changeset
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4 <xref type="bio.tools">quast</xref> |
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481a230d9f1d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
8
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changeset
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5 </xrefs> |
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6
bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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6 <macros> |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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7 <token name="@TOOL_VERSION@">5.0.2</token> |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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8 <xml name="gene_thresholds"> |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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9 <param name="gene_thresholds" argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/> |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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10 </xml> |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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11 </macros> |
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0
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff
changeset
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12 <requirements> |
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6
bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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changeset
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13 <requirement type="package" version="@TOOL_VERSION@">quast</requirement> |
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0
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff
changeset
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14 </requirements> |
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5
844452fe09f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
4
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changeset
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15 <command detect_errors="exit_code"> |
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0
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff
changeset
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16 <![CDATA[ |
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5
844452fe09f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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changeset
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17 #import re |
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6
bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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18 |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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19 #if str($in.custom) == 'false' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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20 #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $in.inputs ]) |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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21 #else |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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22 #set $labels = [] |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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23 #for $x in $in.inputs |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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24 #if str($x.labels) != '' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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25 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels))) |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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26 #else |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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27 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.input.element_identifier))) |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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28 #end if |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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29 #end for |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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30 #set $labels = ','.join($labels) |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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31 #end if |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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32 |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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changeset
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33 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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34 #set $temp_ref_list_fp = 'temp_ref_list_fp' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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35 #set $temp_ref_list_f = open($temp_ref_list_fp, 'w') |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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36 #silent $temp_ref_list_f.write('\n'.join([x.strip() for x in $assembly.ref.references_list.split(',')])) |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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37 #silent $temp_ref_list_f.close() |
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5
844452fe09f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
4
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changeset
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38 #end if |
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6
bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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39 |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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40 #if $assembly.type == 'genome' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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41 quast |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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42 #else |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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43 metaquast |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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44 #end if |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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45 -o outputdir |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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46 |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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changeset
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47 #if $assembly.type == 'genome' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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48 #if $assembly.ref.use_ref == 'true' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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49 -r '$assembly.ref.r' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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50 #if $assembly.ref.features |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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changeset
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51 --features '$assembly.ref.features' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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52 #end if |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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53 #if $assembly.ref.operons |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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changeset
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54 --operons '$assembly.ref.operons' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
diff
changeset
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55 #end if |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
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changeset
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56 #else if $assembly.ref.est_ref_size |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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57 --est-ref-size $assembly.ref.est_ref_size |
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5
844452fe09f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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58 #end if |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
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59 $assembly.orga_type |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
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60 #else |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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changeset
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61 #if $assembly.ref.origin == 'history' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
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62 -r '$assembly.ref.r' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
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63 #else if $assembly.ref.origin == 'list' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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64 --references-list '$temp_ref_list_fp' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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65 #else if $assembly.ref.origin == 'silva' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
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66 --test-no-ref |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
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67 --max-ref-num '$assembly.ref.max_ref_num' |
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5
844452fe09f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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68 #end if |
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844452fe09f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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69 #end if |
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6
bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
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70 --min-contig $min_contig |
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7
e2f831d9d1e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 82c339e6bc07c98765bcfb56f34520ac38648267
iuc
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71 --threads \${GALAXY_SLOTS:-1} |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
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72 $split_scaffolds |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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73 --labels $labels |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
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74 $large |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
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75 $k_mer.k_mer_stats |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
5
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76 #if str($k_mer.k_mer_stats) != '' |
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bf2c7b30dfb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents:
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77 --k-mer-size $k_mer.k_mer_size |
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844452fe09f8
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78 #end if |
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79 $circos |
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80 #if str($genes.gene_finding.tool) != 'none' |
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81 $genes.gene_finding.tool |
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82 #if $genes.gene_finding.tool == '--gene_finding' or $genes.gene_finding.tool == '--glimmer' |
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83 #set $gene_threshold = ','.join([x.strip() for x in str($genes.gene_finding.gene_thresholds).split(',')]) |
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84 --gene-thresholds '$gene_threshold' |
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85 #end if |
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86 #end if |
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87 $genes.rna_finding |
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88 $genes.conserved_genes_finding |
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89 $al.use_all_alignments |
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90 --min-alignment $al.min_alignment |
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91 --min-identity $al.min_identity |
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92 --ambiguity-usage '$al.ambiguity_usage' |
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93 $al.fragmented |
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94 #set $contig_thresholds = ','.join([x.strip() for x in str($contig_thresholds).split(',')]) |
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95 --contig-thresholds '$contig_thresholds' |
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96 $strict_NA |
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97 --extensive-mis-size $extensive_mis_size |
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98 --scaffold-gap-max-size $scaffold_gap_max_size |
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99 --unaligned-part-size $unaligned_part_size |
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100 $skip_unaligned_mis_contigs |
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101 |
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102 #if str($in.custom) == 'false' |
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103 #for $k in $in.inputs |
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104 '$k' |
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105 #end for |
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106 #else |
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107 #for $k in $in.inputs |
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108 '$k.input' |
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109 #end for |
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110 #end if |
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111 |
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112 && mkdir -p '$report_html.files_path' |
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113 && cp outputdir/*.html '$report_html.files_path' |
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114 #if ($assembly.type == 'genome' and $assembly.ref.use_ref) or ($assembly.type == 'metagenome' and $assembly.ref.origin != 'none') |
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115 && cp -R outputdir/icarus_viewers '$report_html.files_path' |
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116 #end if |
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0
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117 ]]> |
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118 </command> |
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119 <inputs> |
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120 <conditional name="in"> |
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121 <param name="custom" type="select" label="Use customized names for the input files?" help="They will be used in reports, plots and logs"> |
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122 <option value="true">Yes, specify custom names for</option> |
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123 <option value="false" selected="true">No, use dataset names</option> |
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124 </param> |
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125 <when value="true"> |
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126 <repeat name="inputs" title="Contigs/scaffolds" min="1"> |
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127 <param name="input" type="data" format="fasta" label="Contigs/scaffolds file"/> |
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128 <param argument="--labels" type="text" value="" label="Name"/> |
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129 </repeat> |
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130 </when> |
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131 <when value="false"> |
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132 <param name="inputs" type="data" format="fasta" multiple="true" label="Contigs/scaffolds file"/> |
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133 </when> |
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134 </conditional> |
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135 <conditional name="assembly"> |
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136 <param name="type" type="select" label="Type of assembly"> |
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137 <option value="genome">Genome</option> |
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138 <option value="metagenome">Metagenome</option> |
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139 </param> |
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140 <when value="genome"> |
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141 <conditional name="ref"> |
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142 <param name="use_ref" type="select" label="Use a reference genome?" help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."> |
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143 <option value="true">Yes</option> |
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144 <option value="false" selected="true">No</option> |
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145 </param> |
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146 <when value="true"> |
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147 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" /> |
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148 <param argument="--features" type="data" format="gff, gff3, bed" optional="true" label="Genomic feature positions in the reference genome" help="Gene coordinates for the reference genome"/> |
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149 <param argument="--operons" type="data" format="gff, gff3, bed" optional="true" label="Operon positions in the reference genome" help="Operon coordinates for the reference genome"/> |
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150 </when> |
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151 <when value="false"> |
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152 <param name="est_ref_size" argument="--est-ref-size" type="integer" optional="true" label="Estimated reference genome size (in bp) for computing NGx statistics" help=""/> |
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153 </when> |
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154 </conditional> |
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155 <param name="orga_type" type="select" label="Type of organism"> |
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156 <option value="">Prokaryotes: use of GeneMarkS for gene finding</option> |
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157 <option value="--eukaryote">Eukaryote (--eukaryote): use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding</option> |
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158 <option value="--fungus">Fungus (--fungus): use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding</option> |
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159 </param> |
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160 </when> |
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161 <when value="metagenome"> |
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162 <conditional name="ref"> |
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163 <param name="origin" type="select" label="Reference genome" help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."> |
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164 <option value="history">From history</option> |
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165 <option value="list">From list</option> |
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166 <option value="silva">From SILVA database</option> |
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167 <option value="none" selected="true">None</option> |
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168 </param> |
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169 <when value="history"> |
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170 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" /> |
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171 </when> |
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172 <when value="list"> |
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173 <param name="references_list" argument="references-list" type="text" value="" label="Comma-separated list of reference genomes" help="MetaQUAST will search for these references in the NCBI database and will download the found ones"/> |
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174 </when> |
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175 <when value="silva"> |
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176 <param name="max_ref_num" argument="-max-ref-num" type="integer" value="50" label="Maximum number of reference genomes (per each assembly) to download after searching in the SILVA databa" /> |
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177 </when> |
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178 <when value="none"/> |
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179 </conditional> |
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180 </when> |
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181 </conditional> |
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182 <param name="min_contig" argument="--min-contig" type="integer" value="500" label="Lower threshold for a contig length (in bp)" help="Shorter contigs won't be taken into account"/> |
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183 <param name="split_scaffolds" argument="--split-scaffolds" type="boolean" truevalue="--split-scaffolds" falsevalue="" checked="false" label="Are assemblies scaffolds rather than contigs?" help="QUAST will add split versions of assemblies to the comparison. Assemblies are split by continuous fragments of N's of length >= 10. If broken version is equal to the original assembly (i.e. nothing was split) it is not included in the comparison."/> |
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184 <param argument="--large" type="boolean" truevalue="--large" falsevalue="" checked="false" label="Is genome large (> 100 Mbp)?" help="Use optimal parameters for evaluation of large genomes. Affects speed and accuracy. In particular, imposes --eukaryote --min-contig 3000 --min-alignment 500 --extensive-mis-size 7000 (can be overridden manually with the corresponding options). In addition, this mode tries to identify misassemblies caused by transposable elements and exclude them from the number of misassemblies."/> |
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185 <conditional name="k_mer"> |
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186 <param name="k_mer_stats" argument="--k-mer-stats" type="select" label="Compute k-mer-based quality metrics?" help="It is recommended for large genomes. This may significantly increase memory and time consumption on large genomes"> |
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187 <option value="--k-mer-stats">Yes</option> |
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188 <option value="" selected="true">No</option> |
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189 </param> |
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190 <when value="--k-mer-stats"> |
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191 <param name="k_mer_size" argument="--k-mer-size" type="integer" value="101" label="Size of k" /> |
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192 </when> |
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193 <when value=""/> |
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194 </conditional> |
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195 <param argument="--circos" type="boolean" truevalue="--circos" falsevalue="" checked="false" label="Draw Circos plot?" help=""/> |
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196 <section name="genes" title="Genes"> |
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197 <conditional name="gene_finding"> |
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198 <param name="tool" type="select" label="Tool for gene prediction" help=""> |
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199 <option value="none">Don't predict genes</option> |
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200 <option value="--gene-finding">GeneMarkS if prokaryotes or GeneMark-ES if eukaryotes or fungi</option> |
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201 <option value="--mgm">MetaGeneMark, specially for metagenomic assembly</option> |
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202 <option value="--glimmer">Glimmer</option> |
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203 </param> |
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204 <when value="none"/> |
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205 <when value="--gene-finding"> |
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206 <expand macro="gene_thresholds"/> |
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207 </when> |
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208 <when value="--mgm"/> |
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209 <when value="--glimmer"> |
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210 <expand macro="gene_thresholds"/> |
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211 </when> |
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212 </conditional> |
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213 <param name="rna_finding" argument="--rna-finding" type="boolean" truevalue="--rna-finding" falsevalue="" checked="false" label="Enables ribosomal RNA gene finding?" help="By default, we assume that the genome is prokaryotic, and Barrnap uses the bacterial database for rRNA prediction. If the genome is eukaryotic (fungal), use --eukaryote (--fungus) option to force Barrnap to work with the eukaryotic (fungal) database. "/> |
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214 <param name="conserved_genes_finding" argument="--conserved-genes-finding" type="boolean" truevalue="--conserved-genes-finding" falsevalue="" checked="false" label="Enables search for Universal Single-Copy Orthologs using BUSCO?" help="By default, we assume that the genome is prokaryotic, and BUSCO uses the bacterial database of orthologs. If the genome is eukaryotic (fungal), use --eukaryote (--fungus) option to force BUSCO to work with the eukaryotic (fungal) database. "/> |
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215 </section> |
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216 <section name="al" title="Alignments"> |
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217 <param name="use_all_alignments" argument="--use-all-alignments" type="boolean" truevalue="--use-all-alignments" falsevalue="" checked="false" label="Use all alignments as in QUAST v.1.*. to compute genome fraction, # genomic features, # operons metrics?" help="By default, QUAST v.2.0 and higher filters out ambiguous and redundant alignments, keeping only one alignment per contig (or one set of non-overlapping or slightly overlapping alignments)"/> |
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218 <param name="min_alignment" argument="--min-alignment" type="integer" value="65" label="Minimum length of alignment" help="Alignments shorter than this value will be filtered. Note that all alignments shorter than 65 bp will be filtered regardless of this threshold."/> |
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219 <param name="min_identity" argument="--min-identity" type="float" value="95.0" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. ote that all alignments with IDY% less than 80.0% will be filtered regardless of this threshold. "/> |
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220 <param name="ambiguity_usage" argument="--ambiguity-usage" type="select" label="How processing equally good alignments of a contig (probably repeats)?" help=""> |
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221 <option value="none">Skip all such alignments</option> |
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222 <option value="one" selected="true">Take only one (the very best one)</option> |
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223 <option value="all">Use all alignments. It can cause a significant increase of # mismatches (repeats are almost always inexact due to accumulated SNPs, indels, etc.). It is useful for metagenomic assemblies where ambiguous alignments might represent homologous sequences of different strains</option> |
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224 </param> |
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225 <param name="ambiguity_score" argument="--ambiguity-score" type="float" value="0.99" min="0.8" max="1.0" label="Score S for defining equally good alignments of a single contig" help="All alignments are sorted by decreasing LEN × IDY% value. All alignments with LEN × IDY% less than S × best(LEN × IDY%) are discarded. "/> |
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226 <param argument="--fragmented" type="boolean" truevalue="--fragmented" falsevalue="" checked="false" label="Use all alignments as in QUAST v.1.*. to compute genome fraction, # genomic features, # operons metrics?" help="By default, QUAST v.2.0 and higher filters out ambiguous and redundant alignments, keeping only one alignment per contig (or one set of non-overlapping or slightly overlapping alignments)"/> |
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227 <param name="fragmented_max_indent" argument="--fragmented-max-indent" type="integer" value="50" label="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments" help="The value should be less than extensive misassembly size"/> |
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228 <param name="upper_bound_assembly" argument="--upper-bound-assembly" type="boolean" truevalue="--upper-bound-assembly" falsevalue="" checked="false" label="Simulate upper bound assembly based on the reference genome and a given set reads?" help="Mate-pairs or long reads, such as Pacbio SMRT/Oxford Nanopore, are REQUIRED. This assembly is added to the comparison and could be useful for estimating the upper bounds of completeness and contiguity that theoretically can be reached by assembly software from this particular set of reads. The concept is based on the fact that the reference genome cannot be completely reconstructed from raw reads due to long genomic repeats and low covered regions. See Mikheenko et al., 2018 for more details. "/> |
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229 <param name="upper_bound_min_con" argument="--upper-bound-min-con" type="integer" value="2" label="Minimal number of 'connecting reads' needed for joining upper bound contigs into a scaffold" help="This is important for a realistic estimation of genome assembly fragmentation due to long repeats. The default values is 2 for mate-pairs and 1 for long reads (PacBio or Nanopore libraries)."/> |
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230 </section> |
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231 <param name="contig_thresholds" argument="--contig-thresholds" type="text" value="0,1000" label="Comma-separated list of contig length thresholds (in bp)" help="Used in # contigs ≥ x and total length (≥ x) metrics"/> |
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232 <param name="strict_NA" argument="--strict-NA" type="boolean" truevalue="--strict-NA" falsevalue="" checked="false" label="Break contigs at every misassembly event (including local ones) to compute NAx and NGAx statistics?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/> |
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233 <param name="extensive_mis_size" argument="--extensive-mis-size" type="integer" value="1000" min="85" label="Lower threshold for the relocation size (gap or overlap size between left and right flanking sequence)" help="Shorter relocations are considered as local misassemblies. It does not affect other types of extensive misassemblies (inversions and translocations). The default value is 1000 bp. Note that the threshold should be greater than maximum indel length which is 85 bp."/> |
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234 <param name="scaffold_gap_max_size" argument="--scaffold-gap-max-size" type="integer" value="1000" label="Max allowed scaffold gap length difference for detecting corresponding type of misassemblies" help="Longer inconsistencies are considered as relocations and thus, counted as extensive misassemblies. The default value is 10000 bp. Note that the threshold make sense only if it is greater than extensive misassembly size"/> |
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235 <param name="unaligned_part_size" argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/> |
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236 <param name="skip_unaligned_mis_contigs" argument="--skip-unaligned-mis-contigs" type="boolean" truevalue="" falsevalue="--skip-unaligned-mis-contigs" checked="true" label="Distinguish contigs with more than 50% unaligned bases as a separate group of contigs?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/> |
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237 </inputs> |
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238 <outputs> |
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239 <data name="quast_tabular" format="tabular" label="${tool.name} on ${on_string}: tabular report" from_work_dir="outputdir/report.tsv"/> |
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240 <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html"/> |
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241 <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF report" from_work_dir="outputdir/report.pdf"/> |
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242 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log"/> |
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243 <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt"> |
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244 <filter>(assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true') or (assembly['type'] == 'metagenome' and assembly['ref']['origin'] != 'none')</filter> |
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245 </data> |
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246 <data name="unalign" format="tabular" label="${tool.name} on ${on_string}: Unaligned contigs" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv"> |
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247 <filter>(assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true') or (assembly['type'] == 'metagenome' and assembly['ref']['origin'] != 'none')</filter> |
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248 </data> |
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249 <data name="kmers" format="tabular" label="${tool.name} on ${on_string}: K-mer-based metrics" from_work_dir="outputdir/k_mer_stats/kmers_report.txt"> |
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250 <filter>k_mer['k_mer_stats'] != ''</filter> |
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251 </data> |
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252 </outputs> |
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253 <tests> |
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254 <test> |
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255 <!-- Test with reference and genes annotations --> |
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256 <conditional name="in"> |
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257 <param name="custom" value="true"/> |
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258 <repeat name="inputs"> |
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259 <param name="input" value="contigs1.fna"/> |
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260 <param name="labels" value="contig1"/> |
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261 </repeat> |
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262 <repeat name="inputs"> |
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263 <param name="input" value="contigs2.fna"/> |
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264 <param name="labels" value=""/> |
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265 </repeat> |
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266 </conditional> |
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267 <conditional name="assembly"> |
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268 <param name="type" value="genome"/> |
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269 <conditional name="ref"> |
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270 <param name="use_ref" value="true"/> |
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271 <param name="r" value="reference.fna"/> |
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272 <param name="features" value="genes.gff"/> |
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273 </conditional> |
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274 <param name="orga_type" value=""/> |
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275 </conditional> |
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276 <param name="min_contig" value="500"/> |
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277 <param name="split_scaffolds" value="false"/> |
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278 <param name="large" value="true"/> |
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279 <conditional name="k_mer"> |
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280 <param name="k_mer_stats" value="--k-mer-stats"/> |
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281 <param name="k_mer_size" value="101" /> |
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282 </conditional> |
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283 <param name="circos" value="true"/> |
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284 <section name="genes"> |
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285 <conditional name="gene_finding"> |
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286 <param name="tool" value="--gene_finding"/> |
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287 <param name="gene_thresholds" value="0,300,1500,3000"/> |
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288 </conditional> |
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289 <param name="rna_finding" value="true"/> |
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290 <param name="conserved_genes_finding" value="true"/> |
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291 </section> |
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292 <section name="al"> |
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293 <param name="use_all_alignments" value="true"/> |
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294 <param name="min_alignment" value="65"/> |
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295 <param name="min_identity" value="95.0"/> |
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296 <param name="ambiguity_usage" value="one"/> |
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297 <param name="ambiguity_score" value="0.99"/> |
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298 <param name="fragmented" value="true"/> |
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299 <param name="fragmented_max_indent" value="50"/> |
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300 <param name="upper_bound_assembly" value="true"/> |
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301 <param name="upper_bound_min_con" value="2"/> |
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302 </section> |
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303 <param name="contig_thresholds" value="0,1000"/> |
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304 <param name="strict_NA" value="true"/> |
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305 <param name="extensive_mis_size" value="1000"/> |
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306 <param name="scaffold_gap_max_size" value="1000"/> |
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307 <param name="unaligned_part_size" value="500"/> |
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308 <param name="skip_unaligned_mis_contigs" value="true"/> |
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309 <output name="quast_tabular" file="test1.tabular" lines_diff="2"/> |
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310 <output name="mis_ass" file="test1_mis_ass.tabular"/> |
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311 <output name="unalign" file="test1_unalign.tabular"/> |
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312 <output name="kmers" file="test1_kmers.tabular"/> |
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313 </test> |
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314 <test> |
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315 <!-- Test without reference --> |
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316 <conditional name="in"> |
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317 <param name="custom" value="false"/> |
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318 <param name="inputs" value="contigs1.fna,contigs2.fna"/> |
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319 </conditional> |
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320 <conditional name="assembly"> |
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321 <param name="type" value="genome"/> |
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322 <conditional name="ref"> |
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323 <param name="use_ref" value="false"/> |
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324 </conditional> |
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325 <param name="orga_type" value="--eukaryote"/> |
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326 </conditional> |
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327 <param name="min_contig" value="500"/> |
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328 <param name="split_scaffolds" value="false"/> |
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329 <param name="large" value="false"/> |
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330 <conditional name="k_mer"> |
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331 <param name="k_mer_stats" value=""/> |
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332 </conditional> |
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333 <param name="circos" value="false"/> |
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334 <section name="genes"> |
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335 <conditional name="gene_finding"> |
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336 <param name="tool" value="none"/> |
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337 </conditional> |
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338 <param name="rna_finding" value="false"/> |
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339 <param name="conserved_genes_finding" value="false"/> |
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340 </section> |
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341 <section name="al"> |
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342 <param name="use_all_alignments" value="false"/> |
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343 <param name="min_alignment" value="65"/> |
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344 <param name="min_identity" value="95.0"/> |
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345 <param name="ambiguity_usage" value="one"/> |
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346 <param name="ambiguity_score" value="0.99"/> |
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347 <param name="fragmented" value="false"/> |
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348 <param name="fragmented_max_indent" value="50"/> |
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349 <param name="upper_bound_assembly" value="false"/> |
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350 <param name="upper_bound_min_con" value="2"/> |
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351 </section> |
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352 <param name="contig_thresholds" value="0,1000, 500"/> |
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353 <param name="strict_NA" value="false"/> |
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354 <param name="extensive_mis_size" value="1000"/> |
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355 <param name="scaffold_gap_max_size" value="1000"/> |
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356 <param name="unaligned_part_size" value="500"/> |
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357 <param name="skip_unaligned_mis_contigs" value="-"/> |
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358 <output name="quast_tabular" file="test2.tabular"/> |
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359 <output name="report_html" file="test2_report.html" compare="sim_size"/> |
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360 <output name="report_pdf" file="test2_report.pdf" compare="sim_size"/> |
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361 </test> |
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362 <test> |
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363 <!-- Test with metagenomics --> |
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364 <conditional name="in"> |
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365 <param name="custom" value="false"/> |
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366 <param name="inputs" value="contigs3.fasta"/> |
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367 </conditional> |
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368 <conditional name="assembly"> |
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369 <param name="type" value="metagenome"/> |
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370 <conditional name="ref"> |
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371 <param name="origin" value="none"/> |
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372 </conditional> |
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373 </conditional> |
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374 <param name="min_contig" value="500"/> |
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375 <param name="split_scaffolds" value="false"/> |
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376 <param name="large" value="false"/> |
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377 <conditional name="k_mer"> |
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378 <param name="k_mer_stats" value=""/> |
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379 </conditional> |
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380 <param name="circos" value="false"/> |
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381 <section name="genes"> |
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382 <conditional name="gene_finding"> |
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383 <param name="tool" value="--mgm"/> |
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384 </conditional> |
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385 <param name="rna_finding" value="false"/> |
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386 <param name="conserved_genes_finding" value="false"/> |
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387 </section> |
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388 <section name="al"> |
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389 <param name="use_all_alignments" value="false"/> |
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390 <param name="min_alignment" value="65"/> |
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391 <param name="min_identity" value="95.0"/> |
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392 <param name="ambiguity_usage" value="one"/> |
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393 <param name="ambiguity_score" value="0.99"/> |
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394 <param name="fragmented" value="false"/> |
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395 <param name="fragmented_max_indent" value="50"/> |
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396 <param name="upper_bound_assembly" value="false"/> |
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397 <param name="upper_bound_min_con" value="2"/> |
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398 </section> |
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399 <param name="contig_thresholds" value="0,1000, 500"/> |
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400 <param name="strict_NA" value="false"/> |
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401 <param name="extensive_mis_size" value="1000"/> |
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402 <param name="scaffold_gap_max_size" value="1000"/> |
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403 <param name="unaligned_part_size" value="500"/> |
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404 <param name="skip_unaligned_mis_contigs" value="-"/> |
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405 <output name="quast_tabular" file="test3.tabular"/> |
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406 </test> |
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407 </tests> |
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408 <help> |
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409 <![CDATA[ |
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410 **What it does** |
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411 |
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412 QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. |
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413 |
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414 If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page <http://quast.sourceforge.net/docs/manual.html>`_. |
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415 |
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416 **Using Quast without reference** |
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417 |
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418 Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs: |
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419 |
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420 * Quast report in HTML format |
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421 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file) |
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422 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format |
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423 * Quast log (a file technical information about Quast tool execution) |
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424 |
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425 The **tab delimited Quast report** will contain the following information:: |
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426 |
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427 Assembly pit_fna cef_fna car_fna |
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428 # contigs (>= 0 bp) 100 91 94 |
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429 # contigs (>= 1000 bp) 62 58 61 |
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430 Total length (>= 0 bp) 6480635 6481216 6480271 |
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431 Total length (>= 1000 bp) 6466917 6468946 6467103 |
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432 # contigs 71 66 70 |
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433 Largest contig 848753 848766 662053 |
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434 Total length 6473173 6474698 6473810 |
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435 GC (%) 66.33 66.33 66.33 |
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436 N50 270269 289027 254671 |
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437 N75 136321 136321 146521 |
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438 L50 7 7 8 |
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439 L75 15 15 16 |
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440 # N's per 100 kbp 0.00 0.00 0.00 |
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441 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
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442 where values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ |
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443 |
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444 **Quast report in HTML format** contains graphs in addition to the above metrics, while **Contig viewer** draws contigs ordered from longest to shortest. This ordering is suitable for comparing only largest contigs or number of contigs longer than a specific threshold. The viewer shows N50 and N75 with color and textual indication. If the reference genome is available or at least approximate genome length is known (see `--est-ref-size`), NG50 and NG75 are also shown. You can also tone down contigs shorter than a specified threshold using Icarus control panel: |
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445 |
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446 .. image:: $PATH_TO_IMAGES/contig_view_noR.png |
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447 :width: 558 |
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448 :height: 412 |
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449 |
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4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
450 Also see `Plot description <http://quast.sourceforge.net/docs/manual.html#sec2>`_ section of the manual. |
|
4
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
451 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
452 **Using Quast with reference** |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
453 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
454 Car, pit, and cef are in fact assemblies of *Pseudomonas aeruginosa* UCBPP-PA14, so we can use its genome as a reference (by supplying a Fasta file containing *P. aeruginosa* pa14 genome to **Reference genome** input box). The following outputs will be produced (note the alignment viewer): |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
455 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
456 * Quast report in HTML format |
|
8
4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
457 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file) |
|
4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
458 * `Alignment viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file) |
|
4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
459 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format |
|
4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
460 * Summary of `misassemblies <http://quast.sourceforge.net/docs/manual.html#sec3.1.2>`_ |
|
4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
461 * Summary of `unaligned contigs <http://quast.sourceforge.net/docs/manual.html#sec3.1.3>`_ |
|
4
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
462 * Quast log (a file technical information about Quast tool execution) |
|
0
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff
changeset
|
463 |
|
4
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
464 With the reference Quast produces a much more comprehensive set of results:: |
|
0
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff
changeset
|
465 |
|
4
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
466 Assembly pit_fna cef_fna car_fna |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
467 # contigs (>= 0 bp) 100 91 94 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
468 # contigs (>= 1000 bp) 62 58 61 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
469 Total length (>= 0 bp) 6480635 6481216 6480271 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
470 Total length (>= 1000 bp) 6466917 6468946 6467103 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
471 # contigs 71 66 70 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
472 Largest contig 848753 848766 662053 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
473 Total length 6473173 6474698 6473810 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
474 Reference length 6537648 6537648 6537648 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
475 GC (%) 66.33 66.33 66.33 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
476 Reference GC (%) 66.29 66.29 66.29 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
477 N50 270269 289027 254671 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
478 NG50 270269 289027 254671 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
479 N75 136321 136321 146521 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
480 NG75 136321 136321 136321 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
481 L50 7 7 8 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
482 LG50 7 7 8 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
483 L75 15 15 16 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
484 LG75 15 15 17 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
485 # misassemblies 0 0 0 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
486 # misassembled contigs 0 0 0 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
487 Misassembled contigs length 0 0 0 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
488 # local misassemblies 1 1 2 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
489 # unaligned mis. contigs 0 0 0 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
490 # unaligned contigs 0 + 0 0 + 0 0 + 0 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
491 part part part |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
492 Unaligned length 0 0 0 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
493 Genome fraction (%) 99.015 99.038 99.025 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
494 Duplication ratio 1.000 1.000 1.000 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
495 # N's per 100 kbp 0.00 0.00 0.00 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
496 # mismatches per 100 kbp 3.82 3.63 3.49 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
497 # indels per 100 kbp 1.19 1.13 1.13 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
498 Largest alignment 848753 848766 662053 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
499 Total aligned length 6473163 6474660 6473792 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
500 NA50 270269 289027 254671 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
501 NGA50 270269 289027 254671 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
502 NA75 136321 136321 146521 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
503 NGA75 136321 136321 136321 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
504 LA50 7 7 8 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
505 LGA50 7 7 8 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
506 LA75 15 15 16 |
|
8
4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
507 LGA75 15 15 17 |
|
0
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff
changeset
|
508 |
|
8
4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
509 where, again, values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_. You can see that this report includes a variety of data that can only be computer against a reference assembly. |
|
4
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
510 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
511 Using reference also produces an **Alignment viewer**: |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
512 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
513 .. image:: $PATH_TO_IMAGES/Align_view.png |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
514 :width: 515 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
515 :height: 395 |
|
d90201633fb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
3
diff
changeset
|
516 |
|
8
4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
517 Alignment viewer highlights regions of interest as, in this case, missassemblies that can potentially point to genome rearrangements (see more `here <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_). |
|
0
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff
changeset
|
518 |
|
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff
changeset
|
519 ]]> |
|
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff
changeset
|
520 </help> |
|
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff
changeset
|
521 |
|
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff
changeset
|
522 <citations> |
|
8
4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
523 <citation type="doi">10.1093/bioinformatics/bty266</citation> |
|
4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
524 <citation type="doi">10.1093/bioinformatics/btw379</citation> |
|
4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
525 <citation type="doi">10.1093/bioinformatics/btv697</citation> |
|
4c2bef52f68e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents:
7
diff
changeset
|
526 <citation type="doi">10.1093/bioinformatics/btt086</citation> |
|
0
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff
changeset
|
527 </citations> |
|
350257634bbb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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changeset
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528 </tool> |