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annotate quast.xml @ 16:84032664991e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
author iuc
date Thu, 02 Mar 2023 10:38:26 +0000
parents 25368452f73b
children c791615bcc55
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rev   line source
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25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
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1 <tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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2 <description>Genome assembly Quality</description>
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bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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3 <macros>
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e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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4 <import>macros.xml</import>
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bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
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5 </macros>
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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6 <expand macro="bio_tools"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
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7 <expand macro='requirements' />
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844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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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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bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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12
16
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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13 #if str($mode.in.custom) == 'false'
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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14 #if $mode.mode == 'individual'
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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15 #set $labels = re.sub('[^\w\-_]', '_', str($mode.in.inputs.element_identifier))
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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16 #else
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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17 #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $mode.in.inputs])
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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18 #end if
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25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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19 echo $labels &&
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bf2c7b30dfb6 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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84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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21 #if $mode.mode == 'individual'
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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22 #if str($mode.in.labels) != ''
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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23 #set $labels = re.sub('[^\w\-_]', '_', str($mode.in.labels))
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bf2c7b30dfb6 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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84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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25 #set $labels = re.sub('[^\w\-_]', '_', str($mode.in.input.element_identifier))
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bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
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26 #end if
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84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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27 #else
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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28 #set $labels = []
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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29 #for $x in $mode.in.inputs
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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30 #if str($x.labels) != ''
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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31 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels)))
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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32 #else
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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33 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.input.element_identifier)))
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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34 #end if
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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35 #end for
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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36 #set $labels = ','.join($labels)
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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37 #end if
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bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
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38 #end if
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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39
bf2c7b30dfb6 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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25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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41 #set $temp_ref_list_fp = 'temp_ref_list'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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42 #for $i in $assembly.ref.references_list.split(',')
25368452f73b 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 &&
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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44 #end for
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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45 #end if
25368452f73b 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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84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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47 #if $mode.reads.reads_option == 'paired'
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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48 #if $mode.mode == 'individual'
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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49 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
84032664991e 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}' &&
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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51 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_2.element_identifier))
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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52 ln -s '$mode.reads.input_2' 'pe2-${identifier}.${mode.reads.input_2.ext}' &&
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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53 #else
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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54 #for $read in $mode.reads.input_1
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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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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84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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57 #end for
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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58 #for $read in $mode.reads.input_2
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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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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84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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61 #end for
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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62 #end if
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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63 #else if $mode.reads.reads_option == 'paired_collection'
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
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64 #if $mode.mode == 'individual'
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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65 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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66 ln -s '$mode.reads.input_1.forward' 'pe1-${identifier}.${mode.reads.input_1.forward.ext}' &&
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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67 ln -s '$mode.reads.input_1.reverse' 'pe2-${identifier}.${mode.reads.input_1.reverse.ext}' &&
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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68 #else
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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69 #for $read in $mode.reads.input_1
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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70 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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71 ln -s '$read.forward' 'pe1-${identifier}.${read.forward.ext}' &&
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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72 ln -s '$read.reverse' 'pe2-${identifier}.${read.reverse.ext}' &&
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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73 #end for
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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74 #end if
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75 #end if
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bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
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76
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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77 #if $assembly.type == 'genome'
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78 quast
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bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
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79 #else
15
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80 metaquast
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bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
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81 #end if
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e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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82
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84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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83 #if $mode.reads.reads_option == 'single'
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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84 #if $mode.mode == 'individual'
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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85 --single '$mode.reads.input_1'
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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86 #else
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87 #for $read in $mode.reads.input_1
15
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88 --single '$read'
16
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parents: 15
diff changeset
89 #end for
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
90 #end if
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91 #else if $mode.reads.reads_option == 'paired'
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92 #if $mode.mode == 'individual'
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93 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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94 --pe1 'pe1-${identifier}.${mode.reads.input_1.ext}'
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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95 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_2.element_identifier))
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
96 --pe2 'pe2-${identifier}.${mode.reads.input_2.ext}'
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
97 #else
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98 #for $read in $mode.reads.input_1
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99 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
15
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100 --pe1 'pe1-${identifier}.${read.ext}'
16
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101 #end for
84032664991e 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))
15
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104 --pe2 'pe2-${identifier}.${read.ext}'
16
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105 #end for
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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106 #end if
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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107 #else if $mode.reads.reads_option == 'paired_collection'
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108 #if $mode.mode == 'individual'
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109 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
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110 --pe1 'pe1-${identifier}.${mode.reads.input_1.forward.ext}'
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111 --pe2 'pe2-${identifier}.${mode.reads.input_1.reverse.ext}'
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112 #else
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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))
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115 --pe1 'pe1-${identifier}.${read.forward.ext}'
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116 --pe2 'pe2-${identifier}.${read.reverse.ext}'
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117 #end for
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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118 #end if
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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'
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122 #else
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123 #for $read in $mode.reads.input_1
15
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124 --pe12 '$read'
16
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125 #end for
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126 #end if
84032664991e 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'
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128 #if $mode.mode == 'individual'
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129 --mp1 '$mode.reads.input_1'
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130 --mp2 '$mode.reads.input_2'
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131 #else
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132 #for $read in $mode.reads.input_1
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133 --mp1 '$read'
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134 #end for
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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135 #for $read in $mode.reads.input_2
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136 --mp2 '$read'
16
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137 #end for
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138 #end if
84032664991e 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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142 #else
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143 #for $read in $mode.reads.input_1
15
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144 --pacbio '$read'
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145 #end for
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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146 #end if
84032664991e 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 $mode.mode == 'individual'
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149 --nanopore '$mode.reads.input_1'
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150 #else
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151 #for $read in $mode.reads.input_1
15
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152 --nanopore '$read'
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153 #end for
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154 #end if
10
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155 #end if
15
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156 --labels '$labels'
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157 -o 'outputdir'
6
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158
bf2c7b30dfb6 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'
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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160 #if $assembly.ref.use_ref == 'true'
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161 -r '$assembly.ref.r'
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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162 #if $assembly.ref.features
15
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163 --features '$assembly.ref.features'
6
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164 #end if
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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165 #if $assembly.ref.operons
15
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166 --operons '$assembly.ref.operons'
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167 #end if
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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168 $assembly.ref.circos
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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169 $assembly.ref.k_mer.k_mer_stats
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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170 #if str($assembly.ref.k_mer.k_mer_stats) != ''
15
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171 --k-mer-size $assembly.ref.k_mer.k_mer_size
6
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172 #end if
bf2c7b30dfb6 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
15
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174 --est-ref-size $assembly.ref.est_ref_size
5
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diff changeset
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
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184 #end if
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185 $assembly.reuse_combined_alignments
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186 #end if
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187 --min-identity $assembly.min_identity
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188 --min-contig $min_contig
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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'
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193 $genes.gene_finding.tool
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194 #if $genes.gene_finding.tool == '--gene_finding' or $genes.gene_finding.tool == '--glimmer'
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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'
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197 #end if
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198 #end if
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199
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200 $genes.rna_finding
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201 $genes.conserved_genes_finding
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202 $alignments.use_all_alignments
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203 --min-alignment $alignments.min_alignment
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204 --ambiguity-usage '$alignments.ambiguity_usage'
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iuc
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205 --ambiguity-score $alignments.ambiguity_score
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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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209 --upper-bound-min-con $alignments.upper_bound_min_con
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210 #end if
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211 #if $alignments.local_mis_size
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iuc
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212 --local-mis-size $alignments.local_mis_size
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213 #end if
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214
e377f054bcd0 "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
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219 #end if
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220
e377f054bcd0 "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'
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223 $advanced.strict_NA
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224 --extensive-mis-size $advanced.extensive_mis_size
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225 --scaffold-gap-max-size $advanced.scaffold_gap_max_size
25368452f73b 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
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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 $advanced.x_for_Nx
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230
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231 #if str($mode.in.custom) == 'false'
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232 #if $mode.mode == 'individual'
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233 '$mode.in.inputs'
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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
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239 #else
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240 #if $mode.mode == 'individual'
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241 '$mode.in.input'
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242 #else
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243 #for $k in $mode.in.inputs
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244 '$k.input'
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245 #end for
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246 #end if
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247 #end if
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248 --threads \${GALAXY_SLOTS:-1}
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249
15
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250 #if $assembly.type == 'genome'
6
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251 && mkdir -p '$report_html.files_path'
5
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252 && cp outputdir/*.html '$report_html.files_path'
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diff changeset
253 #if $assembly.ref.use_ref
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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254 && cp -R outputdir/icarus_viewers '$report_html.files_path'
25368452f73b 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
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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diff changeset
256 #else
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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
25368452f73b 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
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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259 && mkdir -p '$report_html_meta.files_path'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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260 && cp outputdir/combined_reference/*.html '$report_html_meta.files_path'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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261 && if [[ -d "outputdir/icarus_viewers" ]]; then cp -R outputdir/icarus_viewers 'outputdir/combined_reference/'; fi
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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262 && if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '$report_html_meta.files_path'; fi
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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263 && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '$krona.files_path' && cp outputdir/krona_charts/*.html '$krona.files_path'; fi
5
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iuc
parents: 4
diff changeset
264 #end if
15
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parents: 14
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265 ]]></command>
0
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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266 <inputs>
16
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parents: 15
diff changeset
267 <conditional name="mode">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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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)">
84032664991e 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>
84032664991e 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
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
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271 </param>
16
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parents: 15
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272 <when value="individual">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
273 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
274 <expand macro="custom"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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275 <when value="true">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
276 <expand macro="labelled_input"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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277 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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278 <when value="false">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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279 <param name="inputs" type="data" format="fasta" label="Contigs/scaffolds file"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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280 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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281 </conditional>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
282 <conditional name="reads">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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283 <expand macro="reads_option"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
284 <when value="disabled"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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285 <when value="single">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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286 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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287 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
288 <when value="paired">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
289 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #1" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
290 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #2" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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291 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
292 <when value="paired_collection">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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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" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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294 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
295 <when value="paired_interlaced">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
296 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
297 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
298 <when value="mate_paired">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
299 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #1" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
300 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #2" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
301 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
302 <when value="pacbio">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
303 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
304 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
305 <when value="nanopore">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
306 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
307 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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308 </conditional>
6
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
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309 </when>
16
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
310 <when value="co">
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iuc
parents: 15
diff changeset
311 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
312 <expand macro="custom"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
313 <when value="true">
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iuc
parents: 15
diff changeset
314 <repeat name="inputs" title="Contigs/scaffolds" min="1">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
315 <expand macro="labelled_input"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
316 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
317 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
318 <when value="false">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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319 <param name="inputs" type="data" format="fasta" multiple="true" label="Contigs/scaffolds file"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
320 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
321 </conditional>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
322 <conditional name="reads">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
323 <expand macro="reads_option"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
324 <when value="disabled"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
325 <when value="single">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
326 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
327 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
328 <when value="paired">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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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" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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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" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
331 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
332 <when value="paired_collection">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
333 <param name="input_1" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,fasta,fasta.gz" label="FASTQ/FASTA files" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
334 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
335 <when value="paired_interlaced">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
336 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
337 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
338 <when value="mate_paired">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
339 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
340 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
341 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
342 <when value="pacbio">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
343 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
344 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
345 <when value="nanopore">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
346 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
347 </when>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
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348 </conditional>
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
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349 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
350 </conditional>
6
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
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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">
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372 <param argument="--k-mer-size" type="integer" value="101" label="Size of k" />
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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"/>
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377 </when>
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378 <when value="false">
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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=""/>
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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">
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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>
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386 </param>
15
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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">
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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>
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393 <option value="history">From history</option>
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394 <option value="list">From a list</option>
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395 </param>
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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">
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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"/>
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404 </when>
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405 </conditional>
15
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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."/>
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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 ${on_string}: K-mer-based metrics report" from_work_dir="outputdir/k_mer_stats/kmers_report.txt">
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498 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['k_mer']['k_mer_stats'] != ''</filter>
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499 <filter>'tabular' in output_files</filter>
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500 </data>
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501 <data name="circos_output" format="png" from_work_dir="outputdir/circos/circos.png" label="${tool.name} on ${on_string}: Circos plot">
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502 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['circos']</filter>
6
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503 </data>
14
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504 <collection name="metrics_tabular" type="list" label="${tool.name} on ${on_string}: Tabular reports for key metrics" >
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505 <discover_datasets pattern="(?P&lt;designation&gt;.+).tsv" directory="outputdir/summary/TSV/" format="tabular"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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506 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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507 </collection>
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508 <collection name="metrics_pdf" type="list" label="${tool.name} on ${on_string}: PDF reports for key metrics" >
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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509 <discover_datasets pattern="(?P&lt;designation&gt;.+).pdf" directory="outputdir/summary/PDF/" format="pdf"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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510 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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511 </collection>
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512 <data name="krona" format="html" label="${tool.name} on ${on_string}: Krona chart" from_work_dir="outputdir/krona_charts/*.html">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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513 <filter>assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'none' and 'krona' in output_files</filter>
459ceb2ff536 "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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515 </outputs>
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diff changeset
516 <tests>
10
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diff changeset
517 <!-- Test 01: reference, genes annotations and operon coordinates -->
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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518 <test expect_num_outputs="2">
16
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parents: 15
diff changeset
519 <conditional name="mode">
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diff changeset
520 <param name="mode" value="co"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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diff changeset
521 <conditional name="in">
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522 <param name="custom" value="true"/>
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parents: 15
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523 <repeat name="inputs">
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parents: 15
diff changeset
524 <param name="input" value="contigs1.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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525 <param name="labels" value="contig1"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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526 </repeat>
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parents: 15
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527 <repeat name="inputs">
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parents: 15
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528 <param name="input" value="contigs2.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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529 <param name="labels" value="contig2"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
530 </repeat>
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531 </conditional>
6
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parents: 5
diff changeset
532 </conditional>
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parents: 5
diff changeset
533 <conditional name="assembly">
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diff changeset
534 <param name="type" value="genome"/>
bf2c7b30dfb6 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">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
536 <param name="use_ref" value="true"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
537 <param name="r" value="reference.fna"/>
bf2c7b30dfb6 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"/>
10
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parents: 9
diff changeset
539 <param name="operons" value="operons.bed"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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diff changeset
540 <conditional name="k_mer">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
541 <param name="k_mer_stats" value="--k-mer-stats"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
542 <param name="k_mer_size" value="101" />
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
543 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
544 <param name="circos" value="true"/>
6
bf2c7b30dfb6 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>
bf2c7b30dfb6 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=""/>
bf2c7b30dfb6 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>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
550 <section name="genes">
bf2c7b30dfb6 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">
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
15
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parents: 14
diff changeset
557 <param name="min_identity" value="95.0"/>
6
bf2c7b30dfb6 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>
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parents: 9
diff changeset
559 <section name="alignments">
6
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
560 <param name="use_all_alignments" value="true"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
10
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parents: 9
diff changeset
564 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
565 <section name="advanced">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
566 <param name="contig_thresholds" value="0,1000"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
567 <param name="strict_NA" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
568 <param name="extensive_mis_size" value="1000"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
569 <param name="scaffold_gap_max_size" value="1000"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
570 <param name="unaligned_part_size" value="500"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
571 <param name="skip_unaligned_mis_contigs" value="true"/>
6
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
572 <param name="fragmented_max_indent" value="50"/>
bf2c7b30dfb6 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>
10
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parents: 9
diff changeset
574 <param name="output_files" value="html"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
575 <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/>
13
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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parents: 12
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>
10
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parents: 9
diff changeset
578 <!-- Test 02: all outputs -->
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
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579 <test expect_num_outputs="8">
16
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parents: 15
diff changeset
580 <conditional name="mode">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
581 <param name="mode" value="co"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
582 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
583 <param name="custom" value="true"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
584 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
585 <param name="input" value="contigs1.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
586 <param name="labels" value="contig1"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
587 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
588 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
589 <param name="input" value="contigs2.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
590 <param name="labels" value="contig2"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
591 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
592 </conditional>
10
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parents: 9
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593 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
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594 <conditional name="assembly">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
595 <param name="type" value="genome"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
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596 <conditional name="ref">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
597 <param name="use_ref" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
598 <param name="r" value="reference.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
599 <param name="features" value="genes.gff"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
600 <param name="operons" value="operons.bed"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
601 <conditional name="k_mer">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
602 <param name="k_mer_stats" value="--k-mer-stats"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
603 <param name="k_mer_size" value="101" />
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
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604 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
605 <param name="circos" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
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606 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
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607 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
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608 <param name="output_files" value="html,pdf,tabular,log"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
609 <output name="report_html" file="test2_report.html" ftype="html" compare="sim_size"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
610 <output name="report_pdf" file="test2_report.pdf" ftype="pdf" compare="sim_size"/>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
611 <output name="report_tabular" file="test2_report.tab" ftype="tabular"/>
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
612 <output name="log" file="test2.log" ftype="txt" compare="sim_size"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
613 <output name="mis_ass" file="test2_missasemblies.tab" ftype="tabular"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
614 <output name="unalign" file="test2_unaligned.tab" ftype="tabular"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
615 <output name="kmers" file="test2_kmers.tab" ftype="tabular"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
616 <output name="circos_output" file="test2_circos.png" ftype="png" compare="sim_size"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
617 </test>
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parents: 9
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618 <!-- Test 03: without reference -->
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
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619 <test expect_num_outputs="3">
16
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parents: 15
diff changeset
620 <conditional name="mode">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
621 <param name="mode" value="individual"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
622 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
623 <param name="custom" value="false"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
624 <param name="inputs" value="contigs1.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
625 </conditional>
6
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iuc
parents: 5
diff changeset
626 </conditional>
bf2c7b30dfb6 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">
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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">
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
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631 </conditional>
bf2c7b30dfb6 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"/>
15
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parents: 14
diff changeset
633 <param name="min_identity" value="95.0"/>
6
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
634 </conditional>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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">
bf2c7b30dfb6 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">
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
641 </conditional>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
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644 </section>
10
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parents: 9
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645 <section name="alignments">
6
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parents: 5
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646 <param name="use_all_alignments" value="false"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
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648 <param name="ambiguity_usage" value="one"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
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649 <param name="ambiguity_score" value="0.99"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
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651 </section>
10
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parents: 9
diff changeset
652 <section name="advanced">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
653 <param name="contig_thresholds" value="0,1000, 500"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
654 <param name="strict_NA" value="false"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
655 <param name="extensive_mis_size" value="1000"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
656 <param name="scaffold_gap_max_size" value="1000"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
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657 <param name="unaligned_part_size" value="500"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
658 <param name="skip_unaligned_mis_contigs" value="-"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
659 </section>
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parents: 9
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660 <param name="output_files" value="html,pdf,log" />
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
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661 <output name="log" file="test3.log" ftype="txt" compare="sim_size"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
662 <output name="report_html" file="test3_report.html" compare="sim_size"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
663 <output name="report_pdf" file="test3_report.pdf" compare="sim_size"/>
3
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iuc
parents: 2
diff changeset
664 </test>
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
665 <!-- Test 04: metagenomics -->
15
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parents: 14
diff changeset
666 <test expect_num_outputs="3">
16
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parents: 15
diff changeset
667 <conditional name="mode">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
668 <param name="mode" value="individual"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
669 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
670 <param name="custom" value="false"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
671 <param name="inputs" value="contigs3.fasta"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
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672 </conditional>
6
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
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673 </conditional>
bf2c7b30dfb6 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">
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
676 <conditional name="ref">
16
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parents: 15
diff changeset
677 <param name="origin" value="silva"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
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parents: 15
diff changeset
678 <param name="max_ref_num" value="50"/>
6
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
679 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
680 </conditional>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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">
bf2c7b30dfb6 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">
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
687 </conditional>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
690 </section>
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
691 <section name="alignments">
6
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
bf2c7b30dfb6 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"/>
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
698 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
699 <section name="advanced">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
700 <param name="contig_thresholds" value="0,1000, 500"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
701 <param name="strict_NA" value="false"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
702 <param name="extensive_mis_size" value="1000"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
703 <param name="scaffold_gap_max_size" value="1000"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
704 <param name="unaligned_part_size" value="500"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
705 <param name="skip_unaligned_mis_contigs" value="-"/>
6
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
706 </section>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
707 <param name="output_files" value="log,html,tabular"/>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
708 <output name="log_meta" ftype="txt">
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
709 <assert_contents>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
710 <has_text text="Reference genomes are not found" />
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
711 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
712 </output>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
713 <output name="report_tabular_meta" ftype="tabular">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
714 <assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
715 <has_text text="# contigs (>= 0 bp)"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
716 <has_text text="contigs3_fasta"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
717 <has_text text="# N's per 100 kbp"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
718 <has_n_lines n="17"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
719 </assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
720 </output>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
721 <output name="report_html_meta" ftype="html">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
722 <assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
723 <has_text text="Quality Assessment Tool for Genome Assemblies" />
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
724 <has_text text="contigs3_fasta" />
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
725 <has_text text="Statistics without reference" />
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
726 </assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
727 </output>
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
728 </test>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
729 <!-- Test 05: FASTQ read files -->
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
730 <test expect_num_outputs="3">
16
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
731 <conditional name="mode">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
732 <param name="mode" value="co"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
733 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
734 <param name="custom" value="true"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
735 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
736 <param name="input" value="contigs1.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
737 <param name="labels" value="contig1"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
738 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
739 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
740 <param name="input" value="contigs2.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
741 <param name="labels" value="contig2"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
742 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
743 </conditional>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
744 <conditional name="reads">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
745 <param name="reads_option" value="pacbio"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
746 <param name="input_1" value="pacbio_01.fastq,pacbio_02.fastq,pacbio_03.fastq,pacbio_04.fastq"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
747 </conditional>
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
748 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
749 <conditional name="assembly">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
750 <param name="type" value="genome"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
751 <conditional name="ref">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
752 <param name="use_ref" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
753 <param name="r" value="reference.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
754 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
755 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
756 <section name="alignments">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
757 <param name="upper_bound_assembly" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
758 <param name="upper_bound_min_con" value="1"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
759 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
760 <param name="output_files" value="tabular"/>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
761 <output name="report_tabular" file="test5.tab" ftype="tabular"/>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
762 <output name="mis_ass" ftype="tabular">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
763 <assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
764 <has_text text="All statistics are based on contigs of size >= 500 bp"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
765 <has_text text="# scaffold misassemblies"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
766 <has_text text="contig1"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
767 </assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
768 </output>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
769 <output name="unalign" ftype="tabular">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
770 <assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
771 <has_text text="Fully unaligned length"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
772 <has_text text="contig1"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
773 </assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
774 </output>
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
775 </test>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
776 <!-- Test 06: FASTQ.gz read files -->
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
777 <test expect_num_outputs="1">
16
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
778 <conditional name="mode">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
779 <param name="mode" value="co"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
780 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
781 <param name="custom" value="true"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
782 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
783 <param name="input" value="contigs1.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
784 <param name="labels" value="contig1"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
785 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
786 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
787 <param name="input" value="contigs2.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
788 <param name="labels" value="contig2"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
789 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
790 </conditional>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
791 <conditional name="reads">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
792 <param name="reads_option" value="single"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
793 <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
794 </conditional>
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
795 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
796 <param name="output_files" value="tabular"/>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
797 <output name="report_tabular" file="test6.tab" ftype="tabular"/>
6
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
798 </test>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
799 <!-- Test 07: FASTA.gz read files -->
13
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
800 <test expect_num_outputs="1">
16
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
801 <conditional name="mode">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
802 <param name="mode" value="co"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
803 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
804 <param name="custom" value="true"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
805 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
806 <param name="input" value="contigs1.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
807 <param name="labels" value="contig1"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
808 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
809 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
810 <param name="input" value="contigs2.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
811 <param name="labels" value="contig2"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
812 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
813 </conditional>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
814 <conditional name="reads">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
815 <param name="reads_option" value="single"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
816 <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
817 </conditional>
13
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
818 </conditional>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
819 <param name="output_files" value="tabular"/>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
820 <output name="report_tabular" file="test7.tab" ftype="tabular"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
821 </test>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
822 <!-- Test 08: metagenomics all tab outputs-->
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
823 <test expect_num_outputs="3">
16
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
824 <conditional name="mode">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
825 <param name="mode" value="co"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
826 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
827 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
828 <param name="input" value="meta_contigs_1.fasta"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
829 <param name="labels" value="meta_contigs_1"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
830 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
831 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
832 <param name="input" value="meta_contigs_2.fasta"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
833 <param name="labels" value="meta_contigs_2"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
834 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
835 </conditional>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
836 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
837 <conditional name="assembly">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
838 <param name="type" value="metagenome"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
839 <conditional name="ref">
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
840 <param name="origin" value="history"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
841 <param name="r" value="meta_ref_1.fasta,meta_ref_2.fasta,meta_ref_3.fasta"/>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
842 </conditional>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
843 <param name="min_identity" value="95.0"/>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
844 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
845 <param name="min_contig" value="500"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
846 <param name="split_scaffolds" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
847 <param name="large" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
848 <section name="genes">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
849 <conditional name="gene_finding">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
850 <param name="tool" value="none"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
851 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
852 <param name="rna_finding" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
853 <param name="conserved_genes_finding" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
854 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
855 <section name="alignments">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
856 <param name="use_all_alignments" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
857 <param name="min_alignment" value="65"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
858 <param name="ambiguity_usage" value="one"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
859 <param name="ambiguity_score" value="0.99"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
860 <param name="fragmented" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
861 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
862 <section name="advanced">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
863 <param name="contig_thresholds" value="0,1000"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
864 <param name="strict_NA" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
865 <param name="extensive_mis_size" value="1000"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
866 <param name="scaffold_gap_max_size" value="1000"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
867 <param name="unaligned_part_size" value="500"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
868 <param name="skip_unaligned_mis_contigs" value="-"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
869 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
870 <param name="output_files" value="tabular,summary"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
871 <output name="report_tabular_meta" ftype="tabular">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
872 <assert_contents>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
873 <has_text text="# contigs (>= 0 bp)"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
874 <has_text text="meta_ref_3_fasta"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
875 <has_text text="# N's per 100 kbp"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
876 <has_n_lines n="34"/>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
877 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
878 </output>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
879 <output_collection name="metrics_tabular" type="list" count="15"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
880 <output_collection name="metrics_pdf" type="list" count="16"/>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
881 </test>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
882 <!-- Test 09: metagenomics log, html and krona outputs-->
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
883 <test expect_num_outputs="2">
16
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
884 <conditional name="mode">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
885 <param name="mode" value="co"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
886 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
887 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
888 <param name="input" value="meta_contigs_1.fasta"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
889 <param name="labels" value="meta_contigs_1"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
890 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
891 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
892 <param name="input" value="meta_contigs_2.fasta"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
893 <param name="labels" value="meta_contigs_2"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
894 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
895 </conditional>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
896 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
897 <conditional name="assembly">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
898 <param name="type" value="metagenome"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
899 <conditional name="ref">
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
900 <param name="origin" value="list"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
901 <param name="references_list" value="Lactobacillus_delbrueckii_bulgaricus,Lactobacillus_reuteri"/>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
902 </conditional>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
903 <param name="min_identity" value="95.0"/>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
904 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
905 <param name="min_contig" value="500"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
906 <param name="split_scaffolds" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
907 <param name="large" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
908 <section name="genes">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
909 <conditional name="gene_finding">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
910 <param name="tool" value="none"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
911 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
912 <param name="rna_finding" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
913 <param name="conserved_genes_finding" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
914 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
915 <section name="alignments">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
916 <param name="use_all_alignments" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
917 <param name="min_alignment" value="65"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
918 <param name="ambiguity_usage" value="all"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
919 <param name="ambiguity_score" value="0.99"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
920 <param name="fragmented" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
921 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
922 <section name="advanced">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
923 <param name="contig_thresholds" value="0,1000"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
924 <param name="strict_NA" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
925 <param name="extensive_mis_size" value="1000"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
926 <param name="scaffold_gap_max_size" value="1000"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
927 <param name="unaligned_part_size" value="500"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
928 <param name="skip_unaligned_mis_contigs" value="-"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
929 </section>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
930 <param name="output_files" value="html,log"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
931 <output name="report_html_meta" ftype="html">
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
932 <assert_contents>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
933 <has_text text="meta_contigs_2_fasta" />
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
934 <has_text text="combined_reference" />
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
935 <has_text text="Lactobacillus" />
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
936 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
937 </output>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
938 <output name="log_meta" ftype="txt">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
939 <assert_contents>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
940 <has_text text="List of references was provided, starting to download reference genomes from NCBI" />
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
941 <has_text text="Lactobacillus_delbrueckii_bulgaricus" />
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
942 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
943 </output>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
944 </test>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
945 <!-- Test 10: Test new options -->
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
946 <test expect_num_outputs="1">
16
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
947 <conditional name="mode">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
948 <param name="mode" value="co"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
949 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
950 <param name="custom" value="true"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
951 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
952 <param name="input" value="contigs1.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
953 <param name="labels" value="contig1"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
954 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
955 <repeat name="inputs">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
956 <param name="input" value="contigs2.fna"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
957 <param name="labels" value="contig2"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
958 </repeat>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
959 </conditional>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
960 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
961 <section name="alignments">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
962 <param name="local_mis_size" value="210"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
963 </section>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
964 <conditional name="assembly">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
965 <param name="type" value="genome"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
966 <conditional name="ref">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
967 <param name="use_ref" value="false"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
968 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
969 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
970 <section name="advanced">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
971 <param name="report_all_metrics" value="true"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
972 <param name="x_for_Nx" value="80"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
973 </section>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
974 <param name="output_files" value="tabular"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
975 <output name="report_tabular" file="test10_tabular_report.tab" ftype="tabular"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
976 </test>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
977 <!-- Test 11: Test paired fastq.gz inputs -->
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
978 <test expect_num_outputs="1">
16
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
979 <conditional name="mode">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
980 <param name="mode" value="individual"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
981 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
982 <param name="custom" value="true"/>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
983 <param name="input" value="contigs1.fna"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
984 <param name="labels" value="contig1"/>
16
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
985 </conditional>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
986 <conditional name="reads">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
987 <param name="reads_option" value="paired"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
988 <param name="input_1" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
989 <param name="input_2" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
990 </conditional>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
991 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
992 <conditional name="assembly">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
993 <param name="type" value="genome"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
994 <conditional name="ref">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
995 <param name="use_ref" value="false"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
996 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
997 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
998 <param name="output_files" value="tabular"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
999 <output name="report_tabular" ftype="tabular">
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
1000 <assert_contents>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1001 <has_text text="# contigs (>= 0 bp)"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1002 <has_text text="contig1"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1003 <has_text text="# N's per 100 kbp"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1004 <has_n_lines n="22"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1005 </assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1006 </output>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1007 </test>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1008 <!-- Test 12: Test paired-collection fastq.gz inputs -->
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1009 <test expect_num_outputs="1">
16
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1010 <conditional name="mode">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1011 <param name="mode" value="individual"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1012 <conditional name="in">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1013 <param name="custom" value="true"/>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1014 <param name="input" value="contigs1.fna"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1015 <param name="labels" value="contig1"/>
16
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1016 </conditional>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1017 <conditional name="reads">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1018 <param name="reads_option" value="paired_collection"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1019 <param name="input_1">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1020 <collection type="paired">
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1021 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1022 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1023 </collection>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1024 </param>
84032664991e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
iuc
parents: 15
diff changeset
1025 </conditional>
15
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1026 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1027 <conditional name="assembly">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1028 <param name="type" value="genome"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1029 <conditional name="ref">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1030 <param name="use_ref" value="false"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1031 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1032 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1033 <param name="output_files" value="tabular"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1034 <output name="report_tabular" ftype="tabular">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1035 <assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1036 <has_text text="# contigs (>= 0 bp)"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1037 <has_text text="contig1"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1038 <has_text text="# N's per 100 kbp"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 14
diff changeset
1039 <has_n_lines n="15"/>
14
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
1040 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 13
diff changeset
1041 </output>
13
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1042 </test>
16
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1043 <!-- Test 13: Test co-assembly with paired-collection fastq.gz inputs -->
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1044 <test expect_num_outputs="1">
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parents: 15
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1045 <conditional name="mode">
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1046 <param name="mode" value="co"/>
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1047 <conditional name="in">
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1048 <param name="custom" value="false"/>
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1049 <param name="inputs" value="contigs1.fna,contigs2.fna"/>
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1050 </conditional>
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1051 <conditional name="reads">
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1052 <param name="reads_option" value="paired_collection"/>
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1053 <param name="input_1">
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1054 <collection type="list:paired">
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1055 <element name="s1">
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1056 <collection type="paired">
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1057 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
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1058 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
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1059 </collection>
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1060 </element>
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1061 <element name="s2">
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1062 <collection type="paired">
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1063 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
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1064 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
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1065 </collection>
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1066 </element>
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1067 </collection>
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1068 </param>
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1069 </conditional>
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1070 </conditional>
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1071 <conditional name="assembly">
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1072 <param name="type" value="genome"/>
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1073 <conditional name="ref">
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1074 <param name="use_ref" value="false"/>
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1075 </conditional>
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1076 </conditional>
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1077 <param name="output_files" value="tabular"/>
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1078 <output name="report_tabular" ftype="tabular">
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1079 <assert_contents>
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1080 <has_text text="# contigs (>= 0 bp)"/>
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1081 <has_text text="contigs1"/>
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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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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[
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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**
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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
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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
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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::
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1106
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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
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1122 where values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_
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1123
4
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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:
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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
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1130 Also see `Plot description <http://quast.sourceforge.net/docs/manual.html#sec2>`_ section of the manual.
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1131
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1132 **Using Quast with reference**
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1133
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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):
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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)
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1138 * `Alignment viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
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1139 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
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1140 * Summary of `misassemblies <http://quast.sourceforge.net/docs/manual.html#sec3.1.2>`_
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1141 * Summary of `unaligned contigs <http://quast.sourceforge.net/docs/manual.html#sec3.1.3>`_
4
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1142 * Quast log (a file technical information about Quast tool execution)
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1143
4
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1144 With the reference Quast produces a much more comprehensive set of results::
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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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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
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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
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1166 # misassembled contigs 0 0 0
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1167 Misassembled contigs length 0 0 0
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1168 # local misassemblies 1 1 2
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1169 # unaligned mis. contigs 0 0 0
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1170 # unaligned contigs 0 + 0 0 + 0 0 + 0
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1171 part part part
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1172 Unaligned length 0 0 0
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1173 Genome fraction (%) 99.015 99.038 99.025
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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
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1178 Largest alignment 848753 848766 662053
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1179 Total aligned length 6473163 6474660 6473792
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1180 NA50 270269 289027 254671
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1181 NGA50 270269 289027 254671
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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
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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
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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
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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>`_).
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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>