Mercurial > repos > iuc > quast

annotate quast.xml @ 16:a3b35edea53a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
author iuc
date Tue, 12 Nov 2024 12:46:19 +0000
parents 72472698a2df
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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1 <tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>Genome assembly Quality</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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6 <expand macro="bio_tools"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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7 <expand macro='requirements' />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 #import re
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11 #import os
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f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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12
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13 #if str($mode.in.custom) == 'false'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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14 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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15 #set $labels = re.sub('[^\w\-_]', '_', str($mode.in.inputs.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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16 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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17 #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $mode.in.inputs])
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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18 #end if
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19 echo $labels &&
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f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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20 #else
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21 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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22 #if str($mode.in.labels) != ''
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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23 #set $labels = re.sub('[^\w\-_]', '_', str($mode.in.labels))
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f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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24 #else
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25 #set $labels = re.sub('[^\w\-_]', '_', str($mode.in.input.element_identifier))
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f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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26 #end if
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27 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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28 #set $labels = []
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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29 #for $x in $mode.in.inputs
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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30 #if str($x.labels) != ''
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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31 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels)))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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32 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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33 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.input.element_identifier)))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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34 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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35 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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36 #set $labels = ','.join($labels)
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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37 #end if
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f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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38 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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39
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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40 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list'
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41 #set $temp_ref_list_fp = 'temp_ref_list'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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42 #for $i in $assembly.ref.references_list.split(',')
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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43 echo $i >> $temp_ref_list_fp &&
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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44 #end for
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45 #end if
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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46
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47 #if $mode.reads.reads_option == 'paired'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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48 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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49 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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50 ln -s '$mode.reads.input_1' 'pe1-${identifier}.${mode.reads.input_1.ext}' &&
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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51 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_2.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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52 ln -s '$mode.reads.input_2' 'pe2-${identifier}.${mode.reads.input_2.ext}' &&
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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53 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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54 #for $read in $mode.reads.input_1
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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55 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
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56 ln -s '$read' 'pe1-${identifier}.${read.ext}' &&
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57 #end for
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58 #for $read in $mode.reads.input_2
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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59 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
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60 ln -s '$read' 'pe2-${identifier}.${read.ext}' &&
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61 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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62 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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63 #else if $mode.reads.reads_option == 'paired_collection'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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64 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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65 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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66 ln -s '$mode.reads.input_1.forward' 'pe1-${identifier}.${mode.reads.input_1.forward.ext}' &&
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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67 ln -s '$mode.reads.input_1.reverse' 'pe2-${identifier}.${mode.reads.input_1.reverse.ext}' &&
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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68 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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69 #for $read in $mode.reads.input_1
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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70 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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71 ln -s '$read.forward' 'pe1-${identifier}.${read.forward.ext}' &&
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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72 ln -s '$read.reverse' 'pe2-${identifier}.${read.reverse.ext}' &&
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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73 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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74 #end if
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75 #end if
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f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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76
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77 #if $assembly.type == 'genome'
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78 quast
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79 #else
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80 metaquast
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81 #end if
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82
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83 #if $mode.reads.reads_option == 'single'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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84 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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85 --single '$mode.reads.input_1'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
86 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
87 #for $read in $mode.reads.input_1
14
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diff changeset
88 --single '$read'
15
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iuc
parents: 14
diff changeset
89 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
90 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
diff changeset
91 #else if $mode.reads.reads_option == 'paired'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
92 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
93 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
94 --pe1 'pe1-${identifier}.${mode.reads.input_1.ext}'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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95 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_2.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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diff changeset
96 --pe2 'pe2-${identifier}.${mode.reads.input_2.ext}'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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diff changeset
97 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
98 #for $read in $mode.reads.input_1
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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diff changeset
99 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
14
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100 --pe1 'pe1-${identifier}.${read.ext}'
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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101 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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102 #for $read in $mode.reads.input_2
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103 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
14
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104 --pe2 'pe2-${identifier}.${read.ext}'
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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105 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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diff changeset
106 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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diff changeset
107 #else if $mode.reads.reads_option == 'paired_collection'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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108 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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109 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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110 --pe1 'pe1-${identifier}.${mode.reads.input_1.forward.ext}'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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111 --pe2 'pe2-${identifier}.${mode.reads.input_1.reverse.ext}'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
112 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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113 #for $read in $mode.reads.input_1
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114 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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115 --pe1 'pe1-${identifier}.${read.forward.ext}'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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116 --pe2 'pe2-${identifier}.${read.reverse.ext}'
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117 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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118 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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119 #else if $mode.reads.reads_option == 'paired_interlaced'
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120 #if $mode.mode == 'individual'
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121 --pe12 '$mode.reads.input_1'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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122 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
123 #for $read in $mode.reads.input_1
14
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124 --pe12 '$read'
15
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125 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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126 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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127 #else if $mode.reads.reads_option == 'mate_paired'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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128 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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129 --mp1 '$mode.reads.input_1'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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130 --mp2 '$mode.reads.input_2'
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diff changeset
131 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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132 #for $read in $mode.reads.input_1
14
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diff changeset
133 --mp1 '$read'
15
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134 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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135 #for $read in $mode.reads.input_2
14
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136 --mp2 '$read'
15
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137 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
138 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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139 #else if $mode.reads.reads_option == 'pacbio'
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140 #if $mode.mode == 'individual'
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141 --pacbio '$mode.reads.input_1'
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diff changeset
142 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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143 #for $read in $mode.reads.input_1
14
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144 --pacbio '$read'
15
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145 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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146 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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147 #else if $mode.reads.reads_option == 'nanopore'
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148 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
149 --nanopore '$mode.reads.input_1'
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diff changeset
150 #else
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151 #for $read in $mode.reads.input_1
14
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152 --nanopore '$read'
15
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153 #end for
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154 #end if
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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155 #end if
14
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diff changeset
156 --labels '$labels'
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diff changeset
157 -o 'outputdir'
6
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diff changeset
158
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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159 #if $assembly.type == 'genome'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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diff changeset
160 #if $assembly.ref.use_ref == 'true'
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diff changeset
161 -r '$assembly.ref.r'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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diff changeset
162 #if $assembly.ref.features
14
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diff changeset
163 --features '$assembly.ref.features'
6
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diff changeset
164 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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165 #if $assembly.ref.operons
14
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diff changeset
166 --operons '$assembly.ref.operons'
9
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diff changeset
167 #end if
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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diff changeset
168 $assembly.ref.circos
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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diff changeset
169 $assembly.ref.k_mer.k_mer_stats
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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170 #if str($assembly.ref.k_mer.k_mer_stats) != ''
14
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diff changeset
171 --k-mer-size $assembly.ref.k_mer.k_mer_size
6
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diff changeset
172 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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173 #else if $assembly.ref.est_ref_size
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174 --est-ref-size $assembly.ref.est_ref_size
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175 #end if
6
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176 $assembly.orga_type
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177 #else if $assembly.type == 'metagenome'
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178 #if $assembly.ref.origin == 'history'
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179 -r '$assembly.ref.r'
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180 #else if $assembly.ref.origin == 'list'
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181 --references-list '$temp_ref_list_fp'
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182 #else if $assembly.ref.origin == 'silva'
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183 --max-ref-num $assembly.ref.max_ref_num
5
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184 #end if
14
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185 $assembly.reuse_combined_alignments
5
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186 #end if
14
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iuc
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diff changeset
187 --min-identity $assembly.min_identity
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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188 --min-contig $min_contig
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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diff changeset
189 $split_scaffolds
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190 $large
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191
6
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192 #if str($genes.gene_finding.tool) != 'none'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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193 $genes.gene_finding.tool
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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194 #if $genes.gene_finding.tool == '--gene_finding' or $genes.gene_finding.tool == '--glimmer'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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195 #set $gene_threshold = ','.join([x.strip() for x in str($genes.gene_finding.gene_thresholds).split(',')])
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196 --gene-thresholds '$gene_threshold'
6
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197 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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198 #end if
9
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199
14
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200 $genes.rna_finding
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diff changeset
201 $genes.conserved_genes_finding
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iuc
parents: 13
diff changeset
202 $alignments.use_all_alignments
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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203 --min-alignment $alignments.min_alignment
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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204 --ambiguity-usage '$alignments.ambiguity_usage'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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205 --ambiguity-score $alignments.ambiguity_score
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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206 $alignments.fragmented
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207 $alignments.upper_bound_assembly
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208 #if $alignments.upper_bound_min_con
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iuc
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209 --upper-bound-min-con $alignments.upper_bound_min_con
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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210 #end if
14
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iuc
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diff changeset
211 #if $alignments.local_mis_size
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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212 --local-mis-size $alignments.local_mis_size
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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213 #end if
9
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214
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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215 #if $alignments.fragmented
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216 #if $advanced.fragmented_max_indent != ''
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217 --fragmented-max-indent $advanced.fragmented_max_indent
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218 #end if
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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219 #end if
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220
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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221 #set $contig_thresholds = ','.join([x.strip() for x in str($advanced.contig_thresholds).split(',')])
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222 --contig-thresholds '$contig_thresholds'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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diff changeset
223 $advanced.strict_NA
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224 --extensive-mis-size $advanced.extensive_mis_size
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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225 --scaffold-gap-max-size $advanced.scaffold_gap_max_size
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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226 --unaligned-part-size $advanced.unaligned_part_size
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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227 $advanced.skip_unaligned_mis_contigs
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228 $advanced.report_all_metrics
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229 --x-for-Nx $advanced.x_for_Nx
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230
15
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diff changeset
231 #if str($mode.in.custom) == 'false'
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diff changeset
232 #if $mode.mode == 'individual'
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233 '$mode.in.inputs'
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diff changeset
234 #else
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235 #for $k in $mode.in.inputs
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236 '$k'
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237 #end for
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238 #end if
6
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239 #else
15
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240 #if $mode.mode == 'individual'
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diff changeset
241 '$mode.in.input'
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diff changeset
242 #else
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243 #for $k in $mode.in.inputs
14
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244 '$k.input'
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diff changeset
245 #end for
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246 #end if
6
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247 #end if
14
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248 --threads \${GALAXY_SLOTS:-1}
6
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249
14
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diff changeset
250 #if $assembly.type == 'genome'
6
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251 && mkdir -p '$report_html.files_path'
5
81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
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diff changeset
252 && cp outputdir/*.html '$report_html.files_path'
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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diff changeset
253 #if $assembly.ref.use_ref
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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diff changeset
254 && cp -R outputdir/icarus_viewers '$report_html.files_path'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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diff changeset
255 #end if
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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diff changeset
256 #else
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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257 && if [[ -f "outputdir/report.tsv" ]]; then mkdir -p "outputdir/combined_reference/" && cp "outputdir/report.tsv" "outputdir/combined_reference/report.tsv"; fi
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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258 && if [[ -f "outputdir/report.html" ]]; then mkdir -p "outputdir/combined_reference/" && cp outputdir/*.html "outputdir/combined_reference/"; fi
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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diff changeset
259 && mkdir -p '$report_html_meta.files_path'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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diff changeset
260 && cp outputdir/combined_reference/*.html '$report_html_meta.files_path'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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261 && if [[ -d "outputdir/icarus_viewers" ]]; then cp -R outputdir/icarus_viewers 'outputdir/combined_reference/'; fi
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262 && if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '$report_html_meta.files_path'; fi
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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263 && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '$krona.files_path' && cp outputdir/krona_charts/*.html '$krona.files_path'; fi
5
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264 #end if
14
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265 ]]></command>
0
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266 <inputs>
15
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267 <conditional name="mode">
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268 <param name="mode" type="select" label="Assembly mode?" help="Useful to know if contigs have been generated all samples together (co-assembly) or on each sample individually (individual assembly)">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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269 <option value="individual">Individual assembly (1 contig file per sample)</option>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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270 <option value="co" selected="true">Co-assembly (1 contig file for several samples)</option>
6
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271 </param>
15
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272 <when value="individual">
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273 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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274 <expand macro="custom"/>
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275 <when value="true">
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276 <expand macro="labelled_input"/>
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277 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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278 <when value="false">
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279 <param name="inputs" type="data" format="fasta" label="Contigs/scaffolds file"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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280 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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281 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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282 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
diff changeset
283 <expand macro="reads_option"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
diff changeset
284 <when value="disabled"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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285 <when value="single">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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286 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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287 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
288 <when value="paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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289 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #1" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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290 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #2" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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291 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
292 <when value="paired_collection">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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293 <param name="input_1" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fasta,fasta.gz" label="FASTQ/FASTA files" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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294 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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295 <when value="paired_interlaced">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
296 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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297 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
298 <when value="mate_paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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299 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #1" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
300 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #2" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
301 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
302 <when value="pacbio">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
303 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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304 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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305 <when value="nanopore">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
306 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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307 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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308 </conditional>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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309 </when>
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
310 <when value="co">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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diff changeset
311 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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diff changeset
312 <expand macro="custom"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
313 <when value="true">
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diff changeset
314 <repeat name="inputs" title="Contigs/scaffolds" min="1">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
315 <expand macro="labelled_input"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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316 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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317 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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318 <when value="false">
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319 <param name="inputs" type="data" format="fasta" multiple="true" label="Contigs/scaffolds file"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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320 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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321 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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322 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
323 <expand macro="reads_option"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
324 <when value="disabled"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
325 <when value="single">
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326 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
327 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
328 <when value="paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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329 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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330 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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diff changeset
331 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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diff changeset
332 <when value="paired_collection">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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333 <param name="input_1" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,fasta,fasta.gz" label="FASTQ/FASTA files" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
334 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
335 <when value="paired_interlaced">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
336 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
337 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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diff changeset
338 <when value="mate_paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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339 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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340 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
341 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
342 <when value="pacbio">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
343 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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diff changeset
344 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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345 <when value="nanopore">
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346 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
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347 </when>
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348 </conditional>
9
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349 </when>
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350 </conditional>
6
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351 <conditional name="assembly">
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352 <param name="type" type="select" label="Type of assembly">
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353 <option value="genome">Genome</option>
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354 <option value="metagenome">Metagenome</option>
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355 </param>
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356 <when value="genome">
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357 <conditional name="ref">
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358 <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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359 <option value="true">Yes</option>
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360 <option value="false" selected="true">No</option>
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361 </param>
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362 <when value="true">
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363 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
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364 <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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365 <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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366 <conditional name="k_mer">
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367 <param 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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368 <option value="--k-mer-stats">Yes</option>
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369 <option value="" selected="true">No</option>
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370 </param>
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371 <when value="--k-mer-stats">
15
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372 <param argument="--k-mer-size" type="integer" value="101" label="Size of k" />
9
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373 </when>
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374 <when value=""/>
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375 </conditional>
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376 <param argument="--circos" type="boolean" truevalue="--circos" falsevalue="" checked="false" label="Generage Circos plot" help="Plot Circos version of Icarus contig alignment viewer"/>
6
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377 </when>
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378 <when value="false">
9
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379 <param argument="--est-ref-size" type="integer" optional="true" label="Estimated reference genome size (in bp) for computing NGx statistics" help=""/>
6
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380 </when>
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381 </conditional>
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382 <param name="orga_type" type="select" label="Type of organism">
9
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383 <option value="">Prokaryotes: use of GeneMarkS for gene finding (default)</option>
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384 <option value="--eukaryote">Eukaryote: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--eukaryote)</option>
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385 <option value="--fungus">Fungus: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--fungus)</option>
6
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386 </param>
14
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387 <expand macro="min_identity_macros" value="95"/>
6
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388 </when>
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389 <when value="metagenome">
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390 <conditional name="ref">
15
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391 <param name="origin" type="select" label="Reference genome" help="If no reference genomes is provided, the tool will try to identify genome content of the metagenome. By default, it will align contigs to SILVA 16S rRNA database, i.e. FASTA file containing small subunit ribosomal RNA sequences to identify genomes. The reference genomes for the chosen genomes are downloaded from the NCBI database. After that, Quast is run on all of them. Reference genomes with low genome fraction (less than 10%) are removed. The usual MetaQUAST analysis continues with the remaining references.">
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392 <option value="silva" selected="true">From SILVA database</option>
6
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393 <option value="history">From history</option>
15
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394 <option value="list">From a list</option>
6
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395 </param>
15
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396 <when value="silva">
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397 <param 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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398 </when>
6
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399 <when value="history">
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400 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
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401 </when>
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402 <when value="list">
15
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403 <param 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"/>
6
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404 </when>
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405 </conditional>
14
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406 <param argument="--reuse-combined-alignments" type="boolean" truevalue="--reuse-combined-alignments" falsevalue="" checked="false" label="Reuse the alignments on the combined reference" help="Reuse the alignments on the combined reference in the subsequent runs per separate references. That is, the alignment procedure is performed only once (for all assemblies against the combined reference) and does NOT executed for each subgroups of contigs against the corresponding separate reference genomes. In each separate reference run, all precomputed assembly alignments for other references are simply ignored" />
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407 <expand macro="min_identity_macros" value="90"/>
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408 </when>
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409 </conditional>
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410 <param 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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411 <param 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."/>
6
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412 <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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413 <section name="genes" title="Genes">
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414 <conditional name="gene_finding">
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415 <param name="tool" type="select" label="Tool for gene prediction" help="">
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416 <option value="none">Don't predict genes</option>
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417 <option value="--gene-finding">GeneMarkS if prokaryotes or GeneMark-ES if eukaryotes or fungi</option>
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418 <option value="--mgm">MetaGeneMark, specially for metagenomic assembly</option>
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419 <option value="--glimmer">Glimmer</option>
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420 </param>
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421 <when value="none"/>
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422 <when value="--gene-finding">
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423 <expand macro="gene_thresholds"/>
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424 </when>
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425 <when value="--mgm"/>
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426 <when value="--glimmer">
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427 <expand macro="gene_thresholds"/>
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428 </when>
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429 </conditional>
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430 <param 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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431 <param 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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432 </section>
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433 <section name="alignments" title="Alignments">
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434 <param 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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435 <param 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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436 <param argument="--ambiguity-usage" type="select" label="How processing equally good alignments of a contig (probably repeats)?" help="">
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437 <option value="none">Skip all such alignments</option>
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438 <option value="one" selected="true">Take only one (the very best one)</option>
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439 <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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440 </param>
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441 <param 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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442 <param argument="--fragmented" type="boolean" truevalue="--fragmented" falsevalue="" checked="false" label="Fragmented reference genome" help="Reference genome is fragmented (e.g. a scaffold reference). QUAST will try to detect misassemblies caused by the fragmentation and mark them fake (will be excluded from misassemblies). Note: QUAST will not detect misassemblies caused by the linear representation of circular genome "/>
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443 <param argument="--upper-bound-assembly" type="boolean" truevalue="--upper-bound-assembly" falsevalue="" label="Simulate upper bound assembly" help="Simulate upper bound assembly based on the reference genome and a given set reads (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." />
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444 <param argument="--upper-bound-min-con" type="integer" value="" optional="true" 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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445 <param argument="--local-mis-size" type="integer" value="200" optional="true" label="Minimal local misassembly size" help="Lower threshold for the local misassembly size. Shorter inconsistencies are considered as (long) indels. The default value is 200 bp. Note that the threshold should be equal to or lower than minimal extensive misassembly size, which is 1000 bp by default"/>
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446 </section>
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447 <section name="advanced" title="Advanced options">
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448 <param 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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449 <param 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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450 <param 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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451 <param 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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452 <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/>
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453 <param 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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454 <param argument="--fragmented-max-indent" type="integer" min="0" value="" optional="true" label="Fragment max indent" help="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments. The value should be less than extensive misassembly size.Default value is 50. Note: requires --fragmented option" />
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455 <param argument="--report-all-metrics" type="boolean" truevalue="--report-all-metrics" falsevalue="" checked="false" label="Report all metrics" help="Keep all quality metrics in the main report. Usually, all not-relevant metrics are not included in the report, e.g., reference-based metrics in the no-reference mode. Also, if metric values are undefined for all input assemblies, the metric is removed from the report" />
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456 <param argument="--x-for-Nx" type="integer" min="0" max="100" value="90" label="Report Nx, Lx, etc metrics for specific value of 'x'" help="Value of 'x' for Nx, Lx, NGx, NGAx, etc metrics reported in addition to N50, L50, NG50, NGA50, etc" />
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457 </section>
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458 <param name="output_files" type="select" display="checkboxes" optional="true" multiple="true" label="Output files">
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459 <option value="html" selected="true">HTML reports</option>
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460 <option value="pdf">PDF reports</option>
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461 <option value="tabular">Tabular reports</option>
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462 <option value="log">Log file</option>
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463 <option value="summary">Key metric summary (metagenome mode)</option>
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464 <option value="krona">Krona charts (metagenome mode without reference genomes)</option>
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465 </param>
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466 </inputs>
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467 <outputs>
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468 <data name="report_tabular" format="tabular" label="${tool.name} on ${on_string}: tabular report" from_work_dir="outputdir/report.tsv">
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469 <filter>assembly['type'] == 'genome' and 'tabular' in output_files</filter>
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470 </data>
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471 <data name="report_tabular_meta" format="tabular" label="${tool.name} on ${on_string}: tabular report for combined reference genome" from_work_dir="outputdir/combined_reference/report.tsv">
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472 <filter>assembly['type'] == 'metagenome' and 'tabular' in output_files</filter>
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473 </data>
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474 <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html">
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475 <filter>assembly['type'] == 'genome' and 'html' in output_files</filter>
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476 </data>
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477 <data name="report_html_meta" format="html" label="${tool.name} on ${on_string}: HTML report for combined reference genome" from_work_dir="outputdir/combined_reference/report.html">
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478 <filter>assembly['type'] == 'metagenome' and 'html' in output_files</filter>
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479 </data>
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480 <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF report" from_work_dir="outputdir/report.pdf">
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481 <filter>assembly['type'] == 'genome' and 'pdf' in output_files</filter>
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482 </data>
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483 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log">
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484 <filter>assembly['type'] == 'genome' and 'log' in output_files</filter>
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485 </data>
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486 <data name="log_meta" format="txt" label="${tool.name} on ${on_string}: Log Meta" from_work_dir="outputdir/metaquast.log">
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487 <filter>assembly['type'] == 'metagenome' and 'log' in output_files</filter>
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488 </data>
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489 <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies report" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
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490 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
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491 <filter>'tabular' in output_files</filter>
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492 </data>
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493 <data name="unalign" format="tabular" label="${tool.name} on ${on_string}: Unaligned contigs report" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv">
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494 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
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495 <filter>'tabular' in output_files</filter>
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496 </data>
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497 <data name="kmers" format="tabular" label="${tool.name} on ${on_string}: K-mer-based metrics report" from_work_dir="outputdir/k_mer_stats/kmers_report.txt">
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498 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['k_mer']['k_mer_stats'] != ''</filter>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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diff changeset
499 <filter>'tabular' in output_files</filter>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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500 </data>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
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501 <data name="circos_output" format="png" from_work_dir="outputdir/circos/circos.png" label="${tool.name} on ${on_string}: Circos plot">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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502 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['circos']</filter>
6
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503 </data>
13
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504 <collection name="metrics_tabular" type="list" label="${tool.name} on ${on_string}: Tabular reports for key metrics" >
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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505 <discover_datasets pattern="(?P&lt;designation&gt;.+).tsv" directory="outputdir/summary/TSV/" format="tabular"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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506 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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507 </collection>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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508 <collection name="metrics_pdf" type="list" label="${tool.name} on ${on_string}: PDF reports for key metrics" >
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
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509 <discover_datasets pattern="(?P&lt;designation&gt;.+).pdf" directory="outputdir/summary/PDF/" format="pdf"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
510 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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511 </collection>
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512 <data name="krona" format="html" label="${tool.name} on ${on_string}: Krona chart" from_work_dir="outputdir/krona_charts/*.html">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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parents: 12
diff changeset
513 <filter>assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'none' and 'krona' in output_files</filter>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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514 </data>
0
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parents:
diff changeset
515 </outputs>
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516 <tests>
9
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diff changeset
517 <!-- Test 01: reference, genes annotations and operon coordinates -->
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
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518 <test expect_num_outputs="2">
15
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parents: 14
diff changeset
519 <conditional name="mode">
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parents: 14
diff changeset
520 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
diff changeset
521 <conditional name="in">
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parents: 14
diff changeset
522 <param name="custom" value="true"/>
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parents: 14
diff changeset
523 <repeat name="inputs">
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parents: 14
diff changeset
524 <param name="input" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
525 <param name="labels" value="contig1"/>
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parents: 14
diff changeset
526 </repeat>
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parents: 14
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527 <repeat name="inputs">
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parents: 14
diff changeset
528 <param name="input" value="contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
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529 <param name="labels" value="contig2"/>
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parents: 14
diff changeset
530 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
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531 </conditional>
6
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parents: 5
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532 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
533 <conditional name="assembly">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
534 <param name="type" value="genome"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
535 <conditional name="ref">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
536 <param name="use_ref" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
537 <param name="r" value="reference.fna"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
538 <param name="features" value="genes.gff"/>
9
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parents: 8
diff changeset
539 <param name="operons" value="operons.bed"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
540 <conditional name="k_mer">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
541 <param name="k_mer_stats" value="--k-mer-stats"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
542 <param name="k_mer_size" value="101" />
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
543 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
544 <param name="circos" value="true"/>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
545 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
546 <param name="orga_type" value=""/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
547 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
548 <param name="min_contig" value="500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
549 <param name="split_scaffolds" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
550 <section name="genes">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
551 <conditional name="gene_finding">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
552 <param name="tool" value="--gene_finding"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
553 <param name="gene_thresholds" value="0,300,1500,3000"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
554 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
555 <param name="rna_finding" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
556 <param name="conserved_genes_finding" value="true"/>
14
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parents: 13
diff changeset
557 <param name="min_identity" value="95.0"/>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
558 </section>
9
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parents: 8
diff changeset
559 <section name="alignments">
6
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parents: 5
diff changeset
560 <param name="use_all_alignments" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
561 <param name="min_alignment" value="65"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
562 <param name="ambiguity_usage" value="one"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
563 <param name="ambiguity_score" value="0.99"/>
9
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parents: 8
diff changeset
564 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
565 <section name="advanced">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
566 <param name="contig_thresholds" value="0,1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
567 <param name="strict_NA" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
568 <param name="extensive_mis_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
569 <param name="scaffold_gap_max_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
570 <param name="unaligned_part_size" value="500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
571 <param name="skip_unaligned_mis_contigs" value="true"/>
6
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parents: 5
diff changeset
572 <param name="fragmented_max_indent" value="50"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
573 </section>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
574 <param name="output_files" value="html"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
575 <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/>
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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parents: 11
diff changeset
576 <output name="circos_output" file="test1_circos.png" ftype="png" compare="sim_size"/>
0
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parents:
diff changeset
577 </test>
9
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parents: 8
diff changeset
578 <!-- Test 02: all outputs -->
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
579 <test expect_num_outputs="8">
15
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parents: 14
diff changeset
580 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
diff changeset
581 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
diff changeset
582 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
diff changeset
583 <param name="custom" value="true"/>
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parents: 14
diff changeset
584 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
585 <param name="input" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
586 <param name="labels" value="contig1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
587 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
588 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
589 <param name="input" value="contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
590 <param name="labels" value="contig2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
591 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
592 </conditional>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
593 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
594 <conditional name="assembly">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
595 <param name="type" value="genome"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
596 <conditional name="ref">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
597 <param name="use_ref" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
598 <param name="r" value="reference.fna"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
599 <param name="features" value="genes.gff"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
600 <param name="operons" value="operons.bed"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
601 <conditional name="k_mer">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
602 <param name="k_mer_stats" value="--k-mer-stats"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
603 <param name="k_mer_size" value="101" />
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
604 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
605 <param name="circos" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
606 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
607 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
608 <param name="output_files" value="html,pdf,tabular,log"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
609 <output name="report_html" file="test2_report.html" ftype="html" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
610 <output name="report_pdf" file="test2_report.pdf" ftype="pdf" compare="sim_size"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
611 <output name="report_tabular" file="test2_report.tab" ftype="tabular"/>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
612 <output name="log" file="test2.log" ftype="txt" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
613 <output name="mis_ass" file="test2_missasemblies.tab" ftype="tabular"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
614 <output name="unalign" file="test2_unaligned.tab" ftype="tabular"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
615 <output name="kmers" file="test2_kmers.tab" ftype="tabular"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
616 <output name="circos_output" file="test2_circos.png" ftype="png" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
617 </test>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
618 <!-- Test 03: without reference -->
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
619 <test expect_num_outputs="3">
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
620 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
621 <param name="mode" value="individual"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
622 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
623 <param name="custom" value="false"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
624 <param name="inputs" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
625 </conditional>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
626 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
627 <conditional name="assembly">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
628 <param name="type" value="genome"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
629 <conditional name="ref">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
630 <param name="use_ref" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
631 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
632 <param name="orga_type" value="--eukaryote"/>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
633 <param name="min_identity" value="95.0"/>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
634 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
635 <param name="min_contig" value="500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
636 <param name="split_scaffolds" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
637 <param name="large" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
638 <section name="genes">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
639 <conditional name="gene_finding">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
640 <param name="tool" value="none"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
641 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
642 <param name="rna_finding" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
643 <param name="conserved_genes_finding" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
644 </section>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
645 <section name="alignments">
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
646 <param name="use_all_alignments" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
647 <param name="min_alignment" value="65"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
648 <param name="ambiguity_usage" value="one"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
649 <param name="ambiguity_score" value="0.99"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
650 <param name="fragmented" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
651 </section>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
652 <section name="advanced">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
653 <param name="contig_thresholds" value="0,1000, 500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
654 <param name="strict_NA" value="false"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
655 <param name="extensive_mis_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
656 <param name="scaffold_gap_max_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
657 <param name="unaligned_part_size" value="500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
658 <param name="skip_unaligned_mis_contigs" value="-"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
659 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
660 <param name="output_files" value="html,pdf,log" />
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
661 <output name="log" file="test3.log" ftype="txt" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
662 <output name="report_html" file="test3_report.html" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
663 <output name="report_pdf" file="test3_report.pdf" compare="sim_size"/>
3
6fcbee531de6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
iuc
parents: 2
diff changeset
664 </test>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
665 <!-- Test 04: metagenomics -->
14
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iuc
parents: 13
diff changeset
666 <test expect_num_outputs="3">
15
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iuc
parents: 14
diff changeset
667 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
668 <param name="mode" value="individual"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
669 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
670 <param name="custom" value="false"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
671 <param name="inputs" value="contigs3.fasta"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
672 </conditional>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
673 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
674 <conditional name="assembly">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
675 <param name="type" value="metagenome"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
676 <conditional name="ref">
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
677 <param name="origin" value="silva"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
678 <param name="max_ref_num" value="50"/>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
679 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
680 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
681 <param name="min_contig" value="500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
682 <param name="split_scaffolds" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
683 <param name="large" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
684 <section name="genes">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
685 <conditional name="gene_finding">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
686 <param name="tool" value="--mgm"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
687 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
688 <param name="rna_finding" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
689 <param name="conserved_genes_finding" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
690 </section>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
691 <section name="alignments">
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
692 <param name="use_all_alignments" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
693 <param name="min_alignment" value="65"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
694 <param name="min_identity" value="95.0"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
695 <param name="ambiguity_usage" value="one"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
696 <param name="ambiguity_score" value="0.99"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
697 <param name="fragmented" value="false"/>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
698 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
699 <section name="advanced">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
700 <param name="contig_thresholds" value="0,1000, 500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
701 <param name="strict_NA" value="false"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
702 <param name="extensive_mis_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
703 <param name="scaffold_gap_max_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
704 <param name="unaligned_part_size" value="500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
705 <param name="skip_unaligned_mis_contigs" value="-"/>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
706 </section>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
707 <param name="output_files" value="log,html,tabular"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
708 <output name="log_meta" ftype="txt">
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
709 <assert_contents>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
710 <has_text text="Reference genomes are not found" />
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
711 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
712 </output>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
713 <output name="report_tabular_meta" ftype="tabular">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
714 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
715 <has_text text="# contigs (>= 0 bp)"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
716 <has_text text="contigs3_fasta"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
717 <has_text text="# N's per 100 kbp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
718 <has_n_lines n="17"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
719 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
720 </output>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
721 <output name="report_html_meta" ftype="html">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
722 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
723 <has_text text="Quality Assessment Tool for Genome Assemblies" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
724 <has_text text="contigs3_fasta" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
725 <has_text text="Statistics without reference" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
726 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
727 </output>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
728 </test>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
729 <!-- Test 05: FASTQ read files -->
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
730 <test expect_num_outputs="3">
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
731 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
732 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
733 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
734 <param name="custom" value="true"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
735 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
736 <param name="input" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
737 <param name="labels" value="contig1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
738 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
739 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
740 <param name="input" value="contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
741 <param name="labels" value="contig2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
742 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
743 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
744 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
745 <param name="reads_option" value="pacbio"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
746 <param name="input_1" value="pacbio_01.fastq,pacbio_02.fastq,pacbio_03.fastq,pacbio_04.fastq"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
747 </conditional>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
748 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
749 <conditional name="assembly">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
750 <param name="type" value="genome"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
751 <conditional name="ref">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
752 <param name="use_ref" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
753 <param name="r" value="reference.fna"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
754 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
755 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
756 <section name="alignments">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
757 <param name="upper_bound_assembly" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
758 <param name="upper_bound_min_con" value="1"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
759 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
760 <param name="output_files" value="tabular"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
761 <output name="report_tabular" file="test5.tab" ftype="tabular"/>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
762 <output name="mis_ass" ftype="tabular">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
763 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
764 <has_text text="All statistics are based on contigs of size >= 500 bp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
765 <has_text text="# scaffold misassemblies"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
766 <has_text text="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
767 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
768 </output>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
769 <output name="unalign" ftype="tabular">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
770 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
771 <has_text text="Fully unaligned length"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
772 <has_text text="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
773 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
774 </output>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
775 </test>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
776 <!-- Test 06: FASTQ.gz read files -->
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
777 <test expect_num_outputs="1">
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
778 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
779 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
780 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
781 <param name="custom" value="true"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
782 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
783 <param name="input" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
784 <param name="labels" value="contig1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
785 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
786 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
787 <param name="input" value="contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
788 <param name="labels" value="contig2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
789 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
790 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
791 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
792 <param name="reads_option" value="single"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
793 <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
794 </conditional>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
795 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
796 <param name="output_files" value="tabular"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
797 <output name="report_tabular" file="test6.tab" ftype="tabular"/>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
798 </test>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
799 <!-- Test 07: FASTA.gz read files -->
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
800 <test expect_num_outputs="1">
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
801 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
802 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
803 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
804 <param name="custom" value="true"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
805 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
806 <param name="input" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
807 <param name="labels" value="contig1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
808 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
809 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
810 <param name="input" value="contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
811 <param name="labels" value="contig2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
812 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
813 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
814 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
815 <param name="reads_option" value="single"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
816 <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
817 </conditional>
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
818 </conditional>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
819 <param name="output_files" value="tabular"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
820 <output name="report_tabular" file="test7.tab" ftype="tabular"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
821 </test>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
822 <!-- Test 08: metagenomics all tab outputs-->
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
823 <test expect_num_outputs="3">
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
824 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
825 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
826 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
827 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
828 <param name="input" value="meta_contigs_1.fasta"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
829 <param name="labels" value="meta_contigs_1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
830 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
831 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
832 <param name="input" value="meta_contigs_2.fasta"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
833 <param name="labels" value="meta_contigs_2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
834 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
835 </conditional>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
836 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
837 <conditional name="assembly">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
838 <param name="type" value="metagenome"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
839 <conditional name="ref">
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
840 <param name="origin" value="history"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
841 <param name="r" value="meta_ref_1.fasta,meta_ref_2.fasta,meta_ref_3.fasta"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
842 </conditional>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
843 <param name="min_identity" value="95.0"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
844 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
845 <param name="min_contig" value="500"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
846 <param name="split_scaffolds" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
847 <param name="large" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
848 <section name="genes">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
849 <conditional name="gene_finding">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
850 <param name="tool" value="none"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
851 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
852 <param name="rna_finding" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
853 <param name="conserved_genes_finding" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
854 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
855 <section name="alignments">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
856 <param name="use_all_alignments" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
857 <param name="min_alignment" value="65"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
858 <param name="ambiguity_usage" value="one"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
859 <param name="ambiguity_score" value="0.99"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
860 <param name="fragmented" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
861 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
862 <section name="advanced">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
863 <param name="contig_thresholds" value="0,1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
864 <param name="strict_NA" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
865 <param name="extensive_mis_size" value="1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
866 <param name="scaffold_gap_max_size" value="1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
867 <param name="unaligned_part_size" value="500"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
868 <param name="skip_unaligned_mis_contigs" value="-"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
869 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
870 <param name="output_files" value="tabular,summary"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
871 <output name="report_tabular_meta" ftype="tabular">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
872 <assert_contents>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
873 <has_text text="# contigs (>= 0 bp)"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
874 <has_text text="meta_ref_3_fasta"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
875 <has_text text="# N's per 100 kbp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
876 <has_n_lines n="34"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
877 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
878 </output>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
879 <output_collection name="metrics_tabular" type="list" count="15"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
880 <output_collection name="metrics_pdf" type="list" count="16"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
881 </test>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
882 <!-- Test 09: metagenomics log, html and krona outputs-->
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
883 <test expect_num_outputs="2">
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
884 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
885 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
886 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
887 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
888 <param name="input" value="meta_contigs_1.fasta"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
889 <param name="labels" value="meta_contigs_1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
890 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
891 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
892 <param name="input" value="meta_contigs_2.fasta"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
893 <param name="labels" value="meta_contigs_2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
894 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
895 </conditional>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
896 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
897 <conditional name="assembly">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
898 <param name="type" value="metagenome"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
899 <conditional name="ref">
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
900 <param name="origin" value="list"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
901 <param name="references_list" value="Lactobacillus_delbrueckii_bulgaricus,Lactobacillus_reuteri"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
902 </conditional>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
903 <param name="min_identity" value="95.0"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
904 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
905 <param name="min_contig" value="500"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
906 <param name="split_scaffolds" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
907 <param name="large" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
908 <section name="genes">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
909 <conditional name="gene_finding">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
910 <param name="tool" value="none"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
911 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
912 <param name="rna_finding" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
913 <param name="conserved_genes_finding" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
914 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
915 <section name="alignments">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
916 <param name="use_all_alignments" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
917 <param name="min_alignment" value="65"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
918 <param name="ambiguity_usage" value="all"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
919 <param name="ambiguity_score" value="0.99"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
920 <param name="fragmented" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
921 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
922 <section name="advanced">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
923 <param name="contig_thresholds" value="0,1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
924 <param name="strict_NA" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
925 <param name="extensive_mis_size" value="1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
926 <param name="scaffold_gap_max_size" value="1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
927 <param name="unaligned_part_size" value="500"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
928 <param name="skip_unaligned_mis_contigs" value="-"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
929 </section>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
930 <param name="output_files" value="html,log"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
931 <output name="report_html_meta" ftype="html">
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
932 <assert_contents>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
933 <has_text text="meta_contigs_2_fasta" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
934 <has_text text="combined_reference" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
935 <has_text text="Lactobacillus" />
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
936 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
937 </output>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
938 <output name="log_meta" ftype="txt">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
939 <assert_contents>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
940 <has_text text="List of references was provided, starting to download reference genomes from NCBI" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
941 <has_text text="Lactobacillus_delbrueckii_bulgaricus" />
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
942 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
943 </output>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
944 </test>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
945 <!-- Test 10: Test new options -->
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
946 <test expect_num_outputs="1">
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
947 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
948 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
949 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
950 <param name="custom" value="true"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
951 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
952 <param name="input" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
953 <param name="labels" value="contig1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
954 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
955 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
956 <param name="input" value="contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
957 <param name="labels" value="contig2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
958 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
959 </conditional>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
960 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
961 <section name="alignments">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
962 <param name="local_mis_size" value="210"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
963 </section>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
964 <conditional name="assembly">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
965 <param name="type" value="genome"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
966 <conditional name="ref">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
967 <param name="use_ref" value="false"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
968 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
969 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
970 <section name="advanced">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
971 <param name="report_all_metrics" value="true"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
972 <param name="x_for_Nx" value="80"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
973 </section>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
974 <param name="output_files" value="tabular"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
975 <output name="report_tabular" file="test10_tabular_report.tab" ftype="tabular"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
976 </test>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
977 <!-- Test 11: Test paired fastq.gz inputs -->
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
978 <test expect_num_outputs="1">
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
979 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
980 <param name="mode" value="individual"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
981 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
982 <param name="custom" value="true"/>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
983 <param name="input" value="contigs1.fna"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
984 <param name="labels" value="contig1"/>
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
985 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
986 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
987 <param name="reads_option" value="paired"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
988 <param name="input_1" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
989 <param name="input_2" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
990 </conditional>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
991 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
992 <conditional name="assembly">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
993 <param name="type" value="genome"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
994 <conditional name="ref">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
995 <param name="use_ref" value="false"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
996 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
997 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
998 <param name="output_files" value="tabular"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
999 <output name="report_tabular" ftype="tabular">
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
1000 <assert_contents>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1001 <has_text text="# contigs (>= 0 bp)"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1002 <has_text text="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1003 <has_text text="# N's per 100 kbp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1004 <has_n_lines n="22"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1005 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1006 </output>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1007 </test>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1008 <!-- Test 12: Test paired-collection fastq.gz inputs -->
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1009 <test expect_num_outputs="1">
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1010 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1011 <param name="mode" value="individual"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1012 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1013 <param name="custom" value="true"/>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1014 <param name="input" value="contigs1.fna"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1015 <param name="labels" value="contig1"/>
15
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1016 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1017 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1018 <param name="reads_option" value="paired_collection"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1019 <param name="input_1">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1020 <collection type="paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1021 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1022 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1023 </collection>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1024 </param>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 14
diff changeset
1025 </conditional>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1026 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1027 <conditional name="assembly">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1028 <param name="type" value="genome"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1029 <conditional name="ref">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1030 <param name="use_ref" value="false"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1031 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1032 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
1033 <param name="output_files" value="tabular"/>
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parents: 13
diff changeset
1034 <output name="report_tabular" ftype="tabular">
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parents: 13
diff changeset
1035 <assert_contents>
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parents: 13
diff changeset
1036 <has_text text="# contigs (>= 0 bp)"/>
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parents: 13
diff changeset
1037 <has_text text="contig1"/>
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parents: 13
diff changeset
1038 <has_text text="# N's per 100 kbp"/>
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diff changeset
1039 <has_n_lines n="15"/>
13
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diff changeset
1040 </assert_contents>
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diff changeset
1041 </output>
12
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diff changeset
1042 </test>
15
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diff changeset
1043 <!-- Test 13: Test co-assembly with paired-collection fastq.gz inputs -->
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diff changeset
1044 <test expect_num_outputs="1">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
diff changeset
1045 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
diff changeset
1046 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
diff changeset
1047 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
diff changeset
1048 <param name="custom" value="false"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 14
diff changeset
1049 <param name="inputs" value="contigs1.fna,contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
1050 </conditional>
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diff changeset
1051 <conditional name="reads">
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diff changeset
1052 <param name="reads_option" value="paired_collection"/>
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diff changeset
1053 <param name="input_1">
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1054 <collection type="list:paired">
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diff changeset
1055 <element name="s1">
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diff changeset
1056 <collection type="paired">
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diff changeset
1057 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
1058 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
1059 </collection>
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diff changeset
1060 </element>
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parents: 14
diff changeset
1061 <element name="s2">
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diff changeset
1062 <collection type="paired">
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diff changeset
1063 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
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diff changeset
1064 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
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diff changeset
1065 </collection>
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1066 </element>
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diff changeset
1067 </collection>
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diff changeset
1068 </param>
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diff changeset
1069 </conditional>
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diff changeset
1070 </conditional>
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diff changeset
1071 <conditional name="assembly">
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diff changeset
1072 <param name="type" value="genome"/>
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diff changeset
1073 <conditional name="ref">
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diff changeset
1074 <param name="use_ref" value="false"/>
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diff changeset
1075 </conditional>
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1076 </conditional>
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diff changeset
1077 <param name="output_files" value="tabular"/>
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parents: 14
diff changeset
1078 <output name="report_tabular" ftype="tabular">
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diff changeset
1079 <assert_contents>
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1080 <has_text text="# contigs (>= 0 bp)"/>
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parents: 14
diff changeset
1081 <has_text text="contigs1"/>
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parents: 14
diff changeset
1082 <has_text text="# N's per 100 kbp"/>
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1083 <has_n_lines n="22"/>
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1084 </assert_contents>
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diff changeset
1085 </output>
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1086 </test>
0
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1087 </tests>
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1088 <help>
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1089 <![CDATA[
4
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1090 **What it does**
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1091
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1092 QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.
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1093
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1094 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>`_.
4
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1095
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1096 **Using Quast without reference**
0
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1097
4
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1098 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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1099
4
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1100 * Quast report in HTML format
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1101 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
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1102 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
4
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1103 * Quast log (a file technical information about Quast tool execution)
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1104
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1105 The **tab delimited Quast report** will contain the following information::
0
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1106
4
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1107 Assembly pit_fna cef_fna car_fna
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1108 # contigs (>= 0 bp) 100 91 94
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1109 # contigs (>= 1000 bp) 62 58 61
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1110 Total length (>= 0 bp) 6480635 6481216 6480271
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1111 Total length (>= 1000 bp) 6466917 6468946 6467103
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1112 # contigs 71 66 70
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1113 Largest contig 848753 848766 662053
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1114 Total length 6473173 6474698 6473810
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1115 GC (%) 66.33 66.33 66.33
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1116 N50 270269 289027 254671
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1117 N75 136321 136321 146521
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1118 L50 7 7 8
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1119 L75 15 15 16
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1120 # N's per 100 kbp 0.00 0.00 0.00
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1121
8
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1122 where values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_
0
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1123
4
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diff changeset
1124 **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:
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1125
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1126 .. image:: $PATH_TO_IMAGES/contig_view_noR.png
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1127 :width: 558
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1128 :height: 412
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1129
8
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
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1130 Also see `Plot description <http://quast.sourceforge.net/docs/manual.html#sec2>`_ section of the manual.
4
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1131
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1132 **Using Quast with reference**
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1133
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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diff changeset
1134 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):
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1135
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1136 * Quast report in HTML format
8
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1137 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
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1138 * `Alignment viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
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1139 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
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1140 * Summary of `misassemblies <http://quast.sourceforge.net/docs/manual.html#sec3.1.2>`_
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
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1141 * Summary of `unaligned contigs <http://quast.sourceforge.net/docs/manual.html#sec3.1.3>`_
4
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diff changeset
1142 * Quast log (a file technical information about Quast tool execution)
0
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1143
4
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1144 With the reference Quast produces a much more comprehensive set of results::
0
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1145
4
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1146 Assembly pit_fna cef_fna car_fna
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1147 # contigs (>= 0 bp) 100 91 94
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1148 # contigs (>= 1000 bp) 62 58 61
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1149 Total length (>= 0 bp) 6480635 6481216 6480271
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1150 Total length (>= 1000 bp) 6466917 6468946 6467103
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1151 # contigs 71 66 70
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1152 Largest contig 848753 848766 662053
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1153 Total length 6473173 6474698 6473810
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1154 Reference length 6537648 6537648 6537648
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1155 GC (%) 66.33 66.33 66.33
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diff changeset
1156 Reference GC (%) 66.29 66.29 66.29
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1157 N50 270269 289027 254671
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1158 NG50 270269 289027 254671
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1159 N75 136321 136321 146521
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1160 NG75 136321 136321 136321
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1161 L50 7 7 8
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1162 LG50 7 7 8
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1163 L75 15 15 16
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1164 LG75 15 15 17
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1165 # misassemblies 0 0 0
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1166 # misassembled contigs 0 0 0
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1167 Misassembled contigs length 0 0 0
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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diff changeset
1168 # local misassemblies 1 1 2
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1169 # unaligned mis. contigs 0 0 0
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1170 # unaligned contigs 0 + 0 0 + 0 0 + 0
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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diff changeset
1171 part part part
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1172 Unaligned length 0 0 0
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1173 Genome fraction (%) 99.015 99.038 99.025
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1174 Duplication ratio 1.000 1.000 1.000
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1175 # N's per 100 kbp 0.00 0.00 0.00
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1176 # mismatches per 100 kbp 3.82 3.63 3.49
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1177 # indels per 100 kbp 1.19 1.13 1.13
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1178 Largest alignment 848753 848766 662053
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1179 Total aligned length 6473163 6474660 6473792
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1180 NA50 270269 289027 254671
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1181 NGA50 270269 289027 254671
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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1182 NA75 136321 136321 146521
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1183 NGA75 136321 136321 136321
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1184 LA50 7 7 8
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1185 LGA50 7 7 8
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1186 LA75 15 15 16
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1187 LGA75 15 15 17
0
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1188
8
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1189 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
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1190
9
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1191 Using reference also produces an **Alignment viewer**:
4
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1192
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1193 .. image:: $PATH_TO_IMAGES/Align_view.png
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1194 :width: 515
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1195 :height: 395
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1196
8
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1197 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
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1198
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1199 ]]>
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1200 </help>
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1201 <expand macro="citations"/>
0
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1202 </tool>