quast: quast.xml annotate

annotate quast.xml @ 15:25368452f73b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124

author	iuc
date	Fri, 05 Aug 2022 15:20:36 +0000
parents	459ceb2ff536
children	84032664991e

rev	line source
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	1 <tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	2 <description>Genome assembly Quality</description>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	3 <macros>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	4 <import>macros.xml</import>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	5 </macros>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	6 <expand macro="bio_tools"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	7 <expand macro='requirements' />
5 844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	8 <command detect_errors="exit_code">
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	9 <![CDATA[
5 844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	10 #import re
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	11 #import os
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	12
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	13 #if str($in.custom) == 'false'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	14 #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $in.inputs])
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	15 echo $labels &&
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	16 #else
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	17 #set $labels = []
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	18 #for $x in $in.inputs
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	19 #if str($x.labels) != ''
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	20 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels)))
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	21 #else
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	22 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.input.element_identifier)))
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	23 #end if
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	24 #end for
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	25 #set $labels = ','.join($labels)
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	26 #end if
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	27
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	28 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list'
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	29 #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 parents: 14 diff changeset	30 #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 iuc parents: 14 diff changeset	31 echo $i >> $temp_ref_list_fp &&
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	32 #end for
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	33 #end if
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	34
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	35 #if $reads.reads_option == 'paired'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	36 #for $read in $reads.input_1
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	37 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	38 ln -s '$read' 'pe1-${identifier}.${read.ext}' &&
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	39 #end for
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	40 #for $read in $reads.input_2
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	41 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	42 ln -s '$read' 'pe2-${identifier}.${read.ext}' &&
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	43 #end for
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	44 #else if $reads.reads_option == 'paired_collection'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	45 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($reads.input_1.element_identifier))
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	46 ln -s '$reads.input_1.forward' 'pe1-${identifier}.${reads.input_1.forward.ext}' &&
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	47 ln -s '$reads.input_1.reverse' 'pe2-${identifier}.${reads.input_1.reverse.ext}' &&
5 844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	48 #end if
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	49
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	50 #if $assembly.type == 'genome'
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	51 quast
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	52 #else
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	53 metaquast
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	54 #end if
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	55
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	56 #if $reads.reads_option == 'single'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	57 #for $read in $reads.input_1
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	58 --single '$read'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	59 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	60 #else if $reads.reads_option == 'paired'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	61 #for $read in $reads.input_1
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	62 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	63 --pe1 'pe1-${identifier}.${read.ext}'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	64 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	65 #for $read in $reads.input_2
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	66 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	67 --pe2 'pe2-${identifier}.${read.ext}'
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	68 #end for
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	69 #else if $reads.reads_option == 'paired_collection'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	70 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($reads.input_1.element_identifier))
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	71 --pe1 'pe1-${identifier}.${reads.input_1.forward.ext}'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	72 --pe2 'pe2-${identifier}.${reads.input_1.reverse.ext}'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	73 #else if $reads.reads_option == 'paired_interlaced'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	74 #for $read in $reads.input_1
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	75 --pe12 '$read'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	76 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	77 #else if $reads.reads_option == 'mate_paired'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	78 #for $read in $reads.input_1
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	79 --mp1 '$read'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	80 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	81 #for $read in $reads.input_2
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	82 --mp2 '$read'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	83 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	84 #else if $reads.reads_option == 'pacbio'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	85 #for $read in $reads.input_1
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	86 --pacbio '$read'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	87 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	88 #else if $reads.reads_option == 'nanopore'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	89 #for $read in $reads.input_1
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	90 --nanopore '$read'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	91 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	92 #end if
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	93
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	94 --labels '$labels'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	95 -o 'outputdir'
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	96
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	97 #if $assembly.type == 'genome'
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	98 #if $assembly.ref.use_ref == 'true'
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	99 -r '$assembly.ref.r'
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	100 #if $assembly.ref.features
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	101 --features '$assembly.ref.features'
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	102 #end if
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	103 #if $assembly.ref.operons
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	104 --operons '$assembly.ref.operons'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	105 #end if
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	106 $assembly.ref.circos
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	107 $assembly.ref.k_mer.k_mer_stats
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	108 #if str($assembly.ref.k_mer.k_mer_stats) != ''
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	109 --k-mer-size $assembly.ref.k_mer.k_mer_size
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	110 #end if
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	111 #else if $assembly.ref.est_ref_size
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	112 --est-ref-size $assembly.ref.est_ref_size
5 844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	113 #end if
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	114 $assembly.orga_type
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	115 #else if $assembly.type == 'metagenome'
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	116 #if $assembly.ref.origin == 'history'
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	117 -r '$assembly.ref.r'
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	118 #else if $assembly.ref.origin == 'list'
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	119 --references-list '$temp_ref_list_fp'
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	120 #else if $assembly.ref.origin == 'silva'
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	121 --test-no-ref
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	122 --max-ref-num $assembly.ref.max_ref_num
5 844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	123 #end if
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	124 $assembly.reuse_combined_alignments
5 844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	125 #end if
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	126
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	127 --min-identity $assembly.min_identity
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	128
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	129 --min-contig $min_contig
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	130 $split_scaffolds
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	131 $large
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	132
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	133 #if str($genes.gene_finding.tool) != 'none'
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	134 $genes.gene_finding.tool
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	135 #if $genes.gene_finding.tool == '--gene_finding' or $genes.gene_finding.tool == '--glimmer'
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	136 #set $gene_threshold = ','.join([x.strip() for x in str($genes.gene_finding.gene_thresholds).split(',')])
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	137 --gene-thresholds '$gene_threshold'
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	138 #end if
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	139 #end if
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	140
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	141 $genes.rna_finding
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	142 $genes.conserved_genes_finding
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	143 $alignments.use_all_alignments
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	144 --min-alignment $alignments.min_alignment
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	145 --ambiguity-usage '$alignments.ambiguity_usage'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	146 --ambiguity-score $alignments.ambiguity_score
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	147 $alignments.fragmented
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	148 $alignments.upper_bound_assembly
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	149 #if $alignments.upper_bound_min_con
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	150 --upper-bound-min-con $alignments.upper_bound_min_con
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	151 #end if
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	152 #if $alignments.local_mis_size
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	153 --local-mis-size $alignments.local_mis_size
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	154 #end if
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	155
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	156 #if $alignments.fragmented
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	157 #if $advanced.fragmented_max_indent != ''
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	158 --fragmented-max-indent $advanced.fragmented_max_indent
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	159 #end if
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	160 #end if
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	161
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	162 #set $contig_thresholds = ','.join([x.strip() for x in str($advanced.contig_thresholds).split(',')])
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	163 --contig-thresholds '$contig_thresholds'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	164 $advanced.strict_NA
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	165 --extensive-mis-size $advanced.extensive_mis_size
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	166 --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 iuc parents: 14 diff changeset	167 --unaligned-part-size $advanced.unaligned_part_size
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	168 $advanced.skip_unaligned_mis_contigs
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	169 $advanced.report_all_metrics
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	170 --x-for-Nx $advanced.x_for_Nx
3 1dd49661494f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67 iuc parents: 2 diff changeset	171
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	172 #if str($in.custom) == 'false'
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	173 #for $k in $in.inputs
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	174 '$k'
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	175 #end for
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	176 #else
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	177 #for $k in $in.inputs
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	178 '$k.input'
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	179 #end for
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	180 #end if
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	181 --threads \${GALAXY_SLOTS:-1}
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	182
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	183 #if $assembly.type == 'genome'
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	184 && mkdir -p '$report_html.files_path'
5 844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	185 && cp outputdir/*.html '$report_html.files_path'
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	186 #if $assembly.ref.use_ref
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	187 && cp -R outputdir/icarus_viewers '$report_html.files_path'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	188 #end if
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	189 #else
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	190 && 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 iuc parents: 14 diff changeset	191 && 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 iuc parents: 14 diff changeset	192 && mkdir -p '$report_html_meta.files_path'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	193 && cp outputdir/combined_reference/*.html '$report_html_meta.files_path'
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	194 && 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 iuc parents: 14 diff changeset	195 && if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '$report_html_meta.files_path'; fi
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	196 && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '$krona.files_path' && cp outputdir/krona_charts/*.html '$krona.files_path'; fi
5 844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	197 #end if
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	198 ]]></command>
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	199 <inputs>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	200 <conditional name="in">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	201 <param name="custom" type="select" label="Use customized names for the input files?" help="They will be used in reports, plots and logs">
11 801663a3a7ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e8ef230f8e63e7fe37a02ee78e000d1063955052" iuc parents: 10 diff changeset	202 <option value="true">Yes, specify custom names</option>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	203 <option value="false" selected="true">No, use dataset names</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	204 </param>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	205 <when value="true">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	206 <repeat name="inputs" title="Contigs/scaffolds" min="1">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	207 <param name="input" type="data" format="fasta" label="Contigs/scaffolds file"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	208 <param argument="--labels" type="text" value="" label="Name"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	209 </repeat>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	210 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	211 <when value="false">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	212 <param name="inputs" type="data" format="fasta" multiple="true" label="Contigs/scaffolds file"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	213 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	214 </conditional>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	215 <conditional name="reads">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	216 <param name="reads_option" type="select" label="Reads options" help="Currently, the supported read types are Illumina unpaired, paired-end and mate-pair reads, PacBio SMRT, and Oxford Nanopore long reads.">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	217 <option value="disabled">Disabled</option>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	218 <option value="single">Illumina single-end reads</option>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	219 <option value="paired">Illumina paired-end reads</option>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	220 <option value="paired_collection">Illumina paired-end reads in paired collection</option>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	221 <option value="paired_interlaced">Illumina interlaced paired-end reads</option>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	222 <option value="mate_paired">Illumina mate-pair reads</option>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	223 <option value="pacbio">Pacbio SMRT reads</option>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	224 <option value="nanopore">Nanopore reads</option>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	225 </param>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	226 <when value="disabled"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	227 <when value="single">
13 74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	228 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	229 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	230 <when value="paired">
13 74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	231 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	232 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	233 </when>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	234 <when value="paired_collection">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	235 <param name="input_1" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fasta,fasta.gz" label="FASTQ/FASTA files" />
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	236 </when>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	237 <when value="paired_interlaced">
13 74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	238 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	239 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	240 <when value="mate_paired">
13 74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	241 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	242 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	243 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	244 <when value="pacbio">
13 74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	245 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	246 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	247 <when value="nanopore">
13 74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	248 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	249 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	250 </conditional>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	251 <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	252 <param name="type" type="select" label="Type of assembly">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	253 <option value="genome">Genome</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	254 <option value="metagenome">Metagenome</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	255 </param>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	256 <when value="genome">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	257 <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	258 <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.">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	259 <option value="true">Yes</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	260 <option value="false" selected="true">No</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	261 </param>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	262 <when value="true">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	263 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	264 <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"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	265 <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"/>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	266 <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	267 <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">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	268 <option value="--k-mer-stats">Yes</option>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	269 <option value="" selected="true">No</option>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	270 </param>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	271 <when 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	272 <param name="k_mer_size" argument="--k-mer-size" type="integer" value="101" label="Size of k" />
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	273 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	274 <when value=""/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	275 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	276 <param argument="--circos" type="boolean" truevalue="--circos" falsevalue="" checked="false" label="Generage Circos plot" help="Plot Circos version of Icarus contig alignment viewer"/>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	277 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	278 <when 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	279 <param argument="--est-ref-size" type="integer" optional="true" label="Estimated reference genome size (in bp) for computing NGx statistics" help=""/>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	280 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	281 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	282 <param name="orga_type" type="select" label="Type of organism">
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	283 <option value="">Prokaryotes: use of GeneMarkS for gene finding (default)</option>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	284 <option value="--eukaryote">Eukaryote: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--eukaryote)</option>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	285 <option value="--fungus">Fungus: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--fungus)</option>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	286 </param>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	287 <expand macro="min_identity_macros" value="95"/>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	288 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	289 <when value="metagenome">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	290 <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	291 <param name="origin" type="select" label="Reference genome" help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference.">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	292 <option value="history">From history</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	293 <option value="list">From list</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	294 <option value="silva">From SILVA database</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	295 <option value="none" selected="true">None</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	296 </param>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	297 <when value="history">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	298 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	299 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	300 <when value="list">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	301 <param name="references_list" argument="references-list" type="text" value="" label="Comma-separated list of reference genomes" help="MetaQUAST will search for these references in the NCBI database and will download the found ones"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	302 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	303 <when value="silva">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	304 <param name="max_ref_num" argument="-max-ref-num" type="integer" value="50" label="Maximum number of reference genomes (per each assembly) to download after searching in the SILVA databa" />
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	305 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	306 <when value="none"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	307 </conditional>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	308 <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" />
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	309 <expand macro="min_identity_macros" value="90"/>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	310 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	311 </conditional>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	312 <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"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	313 <param argument="--split-scaffolds" type="boolean" truevalue="--split-scaffolds" falsevalue="" checked="false" label="Are assemblies scaffolds rather than contigs?" help="QUAST will add split versions of assemblies to the comparison. Assemblies are split by continuous fragments of N's of length >= 10. If broken version is equal to the original assembly (i.e. nothing was split) it is not included in the comparison."/>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	314 <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."/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	315 <section name="genes" title="Genes">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	316 <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	317 <param name="tool" type="select" label="Tool for gene prediction" help="">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	318 <option value="none">Don't predict genes</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	319 <option value="--gene-finding">GeneMarkS if prokaryotes or GeneMark-ES if eukaryotes or fungi</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	320 <option value="--mgm">MetaGeneMark, specially for metagenomic assembly</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	321 <option value="--glimmer">Glimmer</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	322 </param>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	323 <when value="none"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	324 <when value="--gene-finding">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	325 <expand macro="gene_thresholds"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	326 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	327 <when value="--mgm"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	328 <when value="--glimmer">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	329 <expand macro="gene_thresholds"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	330 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	331 </conditional>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	332 <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. "/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	333 <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. "/>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	334 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	335 <section name="alignments" title="Alignments">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	336 <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)"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	337 <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."/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	338 <param argument="--ambiguity-usage" type="select" label="How processing equally good alignments of a contig (probably repeats)?" help="">
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	339 <option value="none">Skip all such alignments</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	340 <option value="one" selected="true">Take only one (the very best one)</option>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	341 <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>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	342 </param>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	343 <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. "/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	344 <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 "/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	345 <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." />
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	346 <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)"/>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	347 <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"/>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	348 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	349 <section name="advanced" title="Advanced options">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	350 <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"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	351 <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)."/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	352 <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."/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	353 <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"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	354 <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	355 <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)."/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	356 <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" />
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	357 <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" />
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	358 <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" />
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	359 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	360 <param name="output_files" type="select" display="checkboxes" optional="true" multiple="true" label="Output files">
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	361 <option value="html" selected="true">HTML reports</option>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	362 <option value="pdf">PDF reports</option>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	363 <option value="tabular">Tabular reports</option>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	364 <option value="log">Log file</option>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	365 <option value="summary">Key metric summary (metagenome mode)</option>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	366 <option value="krona">Krona charts (metagenome mode without reference genomes)</option>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	367 </param>
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	368 </inputs>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	369 <outputs>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	370 <data name="report_tabular" format="tabular" label="${tool.name} on ${on_string}: tabular report" from_work_dir="outputdir/report.tsv">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	371 <filter>assembly['type'] == 'genome' and 'tabular' in output_files</filter>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	372 </data>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	373 <data name="report_tabular_meta" format="tabular" label="${tool.name} on ${on_string}: tabular report for combined reference genome" from_work_dir="outputdir/combined_reference/report.tsv">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	374 <filter>assembly['type'] == 'metagenome' and 'tabular' in output_files</filter>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	375 </data>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	376 <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html">
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	377 <filter>assembly['type'] == 'genome' and 'html' in output_files</filter>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	378 </data>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	379 <data name="report_html_meta" format="html" label="${tool.name} on ${on_string}: HTML report for combined reference genome" from_work_dir="outputdir/combined_reference/report.html">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	380 <filter>assembly['type'] == 'metagenome' and 'html' in output_files</filter>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	381 </data>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	382 <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF report" from_work_dir="outputdir/report.pdf">
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	383 <filter>assembly['type'] == 'genome' and 'pdf' in output_files</filter>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	384 </data>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	385 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log">
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	386 <filter>assembly['type'] == 'genome' and 'log' in output_files</filter>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	387 </data>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	388 <data name="log_meta" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/metaquast.log">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	389 <filter>assembly['type'] == 'metagenome' and 'log' in output_files</filter>
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	390 </data>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	391 <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies report" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	392 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	393 <filter>'tabular' in output_files</filter>
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	394 </data>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	395 <data name="unalign" format="tabular" label="${tool.name} on ${on_string}: Unaligned contigs report" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	396 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	397 <filter>'tabular' in output_files</filter>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	398 </data>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	399 <data name="kmers" format="tabular" label="${tool.name} on ${on_string}: K-mer-based metrics report" from_work_dir="outputdir/k_mer_stats/kmers_report.txt">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	400 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['k_mer']['k_mer_stats'] != ''</filter>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	401 <filter>'tabular' in output_files</filter>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	402 </data>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	403 <data name="circos_output" format="png" from_work_dir="outputdir/circos/circos.png" label="${tool.name} on ${on_string}: Circos plot">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	404 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['circos']</filter>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	405 </data>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	406 <collection name="metrics_tabular" type="list" label="${tool.name} on ${on_string}: Tabular reports for key metrics" >
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	407 <discover_datasets pattern="(?P<designation>.+).tsv" directory="outputdir/summary/TSV/" format="tabular"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	408 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	409 </collection>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	410 <collection name="metrics_pdf" type="list" label="${tool.name} on ${on_string}: PDF reports for key metrics" >
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	411 <discover_datasets pattern="(?P<designation>.+).pdf" directory="outputdir/summary/PDF/" format="pdf"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	412 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	413 </collection>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	414 <data name="krona" format="html" label="${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" iuc parents: 13 diff changeset	415 <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" iuc parents: 13 diff changeset	416 </data>
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	417 </outputs>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	418 <tests>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	419 <!-- 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" iuc parents: 9 diff changeset	420 <test expect_num_outputs="2">
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	421 <conditional name="in">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	422 <param name="custom" value="true"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	423 <repeat name="inputs">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	424 <param name="input" value="contigs1.fna"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	425 <param name="labels" value="contig1"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	426 </repeat>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	427 <repeat name="inputs">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	428 <param name="input" value="contigs2.fna"/>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	429 <param name="labels" value="contig2"/>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	430 </repeat>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	431 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	432 <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	433 <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	434 <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	435 <param name="use_ref" value="true"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	436 <param name="r" value="reference.fna"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	437 <param name="features" value="genes.gff"/>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	438 <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	439 <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	440 <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	441 <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 diff changeset	442 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	443 <param name="circos" value="true"/>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	444 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	445 <param name="orga_type" value=""/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	446 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	447 <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	448 <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	449 <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	450 <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	451 <param name="tool" value="--gene_finding"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	452 <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 iuc parents: 5 diff changeset	453 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	454 <param name="rna_finding" value="true"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	455 <param name="conserved_genes_finding" 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	456 <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 iuc parents: 5 diff changeset	457 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	458 <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	459 <param name="use_all_alignments" value="true"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	460 <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	461 <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	462 <param name="ambiguity_score" value="0.99"/>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	463 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	464 <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	465 <param name="contig_thresholds" value="0,1000"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	466 <param name="strict_NA" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	467 <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	468 <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	469 <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	470 <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 iuc parents: 5 diff changeset	471 <param name="fragmented_max_indent" value="50"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	472 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	473 <param name="output_files" value="html"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	474 <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" iuc parents: 12 diff changeset	475 <output name="circos_output" file="test1_circos.png" ftype="png" compare="sim_size"/>
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	476 </test>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	477 <!-- Test 02: all outputs -->
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	478 <test expect_num_outputs="8">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	479 <conditional name="in">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	480 <param name="custom" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	481 <repeat name="inputs">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	482 <param name="input" value="contigs1.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	483 <param name="labels" value="contig1"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	484 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	485 <repeat name="inputs">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	486 <param name="input" value="contigs2.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	487 <param name="labels" value="contig2"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	488 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	489 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	490 <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	491 <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	492 <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	493 <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	494 <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	495 <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	496 <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	497 <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	498 <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	499 <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 diff changeset	500 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	501 <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 diff changeset	502 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	503 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	504 <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	505 <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	506 <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	507 <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	508 <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	509 <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	510 <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	511 <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" iuc parents: 9 diff changeset	512 <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" iuc parents: 9 diff changeset	513 </test>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	514 <!-- Test 03: without reference -->
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	515 <test expect_num_outputs="3">
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	516 <conditional name="in">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	517 <param name="custom" value="false"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	518 <param name="inputs" value="contigs1.fna,contigs2.fna"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	519 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	520 <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	521 <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	522 <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	523 <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 diff changeset	524 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	525 <param name="orga_type" value="--eukaryote"/>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	526 <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 iuc parents: 5 diff changeset	527 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	528 <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	529 <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	530 <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	531 <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	532 <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	533 <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	534 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	535 <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	536 <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	537 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	538 <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	539 <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	540 <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	541 <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	542 <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	543 <param name="fragmented" value="false"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	544 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	545 <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	546 <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	547 <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	548 <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	549 <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	550 <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	551 <param name="skip_unaligned_mis_contigs" value="-"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	552 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	553 <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" iuc parents: 9 diff changeset	554 <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" iuc parents: 9 diff changeset	555 <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	556 <output name="report_pdf" file="test3_report.pdf" compare="sim_size"/>
3 1dd49661494f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67 iuc parents: 2 diff changeset	557 </test>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	558 <!-- Test 04: metagenomics -->
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	559 <test expect_num_outputs="3">
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	560 <conditional name="in">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	561 <param name="custom" value="false"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	562 <param name="inputs" value="contigs3.fasta"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	563 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	564 <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	565 <param name="type" value="metagenome"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	566 <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	567 <param name="origin" value="none"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	568 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	569 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	570 <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	571 <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	572 <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	573 <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	574 <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	575 <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	576 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	577 <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	578 <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	579 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	580 <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	581 <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	582 <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	583 <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	584 <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	585 <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	586 <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	587 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	588 <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	589 <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	590 <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	591 <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	592 <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	593 <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	594 <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	595 </section>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	596 <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	597 <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	598 <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	599 <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	600 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	601 </output>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	602 <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	603 <assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	604 <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	605 <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	606 <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	607 <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	608 </assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	609 </output>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	610 <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	611 <assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	612 <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	613 <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	614 <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	615 </assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	616 </output>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	617 </test>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	618 <!-- 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	619 <test expect_num_outputs="3">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	620 <conditional name="in">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	621 <param name="custom" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	622 <repeat name="inputs">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	623 <param name="input" value="contigs1.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	624 <param name="labels" value="contig1"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	625 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	626 <repeat name="inputs">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	627 <param name="input" value="contigs2.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	628 <param name="labels" value="contig2"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	629 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	630 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	631 <conditional name="reads">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	632 <param name="reads_option" value="pacbio"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	633 <param name="input_1" value="pacbio_01.fastq,pacbio_02.fastq,pacbio_03.fastq,pacbio_04.fastq"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	634 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	635 <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	636 <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	637 <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	638 <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	639 <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	640 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	641 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	642 <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	643 <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	644 <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	645 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	646 <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	647 <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	648 <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	649 <assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	650 <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	651 <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	652 <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	653 </assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	654 </output>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	655 <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	656 <assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	657 <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	658 <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	659 </assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	660 </output>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	661 </test>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	662 <!-- 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	663 <test expect_num_outputs="1">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	664 <conditional name="in">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	665 <param name="custom" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	666 <repeat name="inputs">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	667 <param name="input" value="contigs1.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	668 <param name="labels" value="contig1"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	669 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	670 <repeat name="inputs">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	671 <param name="input" value="contigs2.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	672 <param name="labels" value="contig2"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	673 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	674 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	675 <conditional name="reads">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	676 <param name="reads_option" value="single"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	677 <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	678 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	679 <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	680 <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	681 </test>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	682 <!-- 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	683 <test expect_num_outputs="1">
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	684 <conditional name="in">
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	685 <param name="custom" value="true"/>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	686 <repeat name="inputs">
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	687 <param name="input" value="contigs1.fna"/>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	688 <param name="labels" value="contig1"/>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	689 </repeat>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	690 <repeat name="inputs">
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	691 <param name="input" value="contigs2.fna"/>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	692 <param name="labels" value="contig2"/>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	693 </repeat>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	694 </conditional>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	695 <conditional name="reads">
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	696 <param name="reads_option" value="single"/>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	697 <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	698 </conditional>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	699 <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	700 <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	701 </test>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	702 <!-- 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	703 <test expect_num_outputs="3">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	704 <conditional name="in">
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	705 <repeat name="inputs">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	706 <param name="input" value="meta_contigs_1.fasta"/>
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="labels" value="meta_contigs_1"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	708 </repeat>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	709 <repeat name="inputs">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	710 <param name="input" value="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	711 <param name="labels" value="meta_contigs_2"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	712 </repeat>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	713 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	714 <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	715 <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	716 <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	717 <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	718 <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	719 </conditional>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	720 <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	721 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	722 <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	723 <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	724 <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	725 <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	726 <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	727 <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	728 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	729 <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	730 <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	731 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	732 <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	733 <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	734 <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	735 <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	736 <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	737 <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	738 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	739 <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	740 <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	741 <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	742 <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	743 <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	744 <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	745 <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	746 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	747 <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	748 <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	749 <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	750 <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	751 <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	752 <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	753 <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	754 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	755 </output>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	756 <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	757 <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	758 </test>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	759 <!-- 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	760 <test expect_num_outputs="2">
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	761 <conditional name="in">
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	762 <repeat name="inputs">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	763 <param name="input" value="meta_contigs_1.fasta"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	764 <param name="labels" value="meta_contigs_1"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	765 </repeat>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	766 <repeat name="inputs">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	767 <param name="input" value="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	768 <param name="labels" value="meta_contigs_2"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	769 </repeat>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	770 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	771 <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	772 <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	773 <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	774 <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	775 <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	776 </conditional>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	777 <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	778 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	779 <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	780 <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	781 <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	782 <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	783 <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	784 <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	785 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	786 <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	787 <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	788 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	789 <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	790 <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	791 <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	792 <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	793 <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	794 <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	795 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	796 <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	797 <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	798 <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	799 <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	800 <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	801 <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	802 <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	803 </section>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	804 <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	805 <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	806 <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	807 <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	808 <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	809 <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	810 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	811 </output>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	812 <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	813 <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	814 <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	815 <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	816 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	817 </output>
15 25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	818 </test>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	819 <!-- 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	820 <test expect_num_outputs="1">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	821 <conditional name="in">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	822 <param name="custom" value="true"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	823 <repeat name="inputs">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	824 <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	825 <param name="labels" value="contig1"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	826 </repeat>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	827 <repeat name="inputs">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	828 <param name="input" value="contigs2.fna"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	829 <param name="labels" value="contig2"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	830 </repeat>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	831 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	832 <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	833 <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	834 </section>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	835 <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	836 <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	837 <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	838 <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	839 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	840 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	841 <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	842 <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	843 <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	844 </section>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	845 <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	846 <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	847 </test>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	848 <!-- 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	849 <test expect_num_outputs="1">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	850 <conditional name="in">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	851 <param name="custom" value="true"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	852 <repeat name="inputs">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	853 <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	854 <param name="labels" value="contig1"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	855 </repeat>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	856 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	857 <conditional name="reads">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	858 <param name="reads_option" value="paired"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	859 <param name="input_1" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	860 <param name="input_2" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	861 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	862 <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	863 <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	864 <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	865 <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	866 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	867 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	868 <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	869 <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	870 <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	871 <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	872 <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	873 <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	874 <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	875 </assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	876 </output>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	877 </test>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	878 <!-- 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	879 <test expect_num_outputs="1">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	880 <conditional name="in">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	881 <param name="custom" value="true"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	882 <repeat name="inputs">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	883 <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	884 <param name="labels" value="contig1"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	885 </repeat>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	886 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	887 <conditional name="reads">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	888 <param name="reads_option" value="paired_collection"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	889 <param name="input_1">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	890 <collection type="paired">
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	891 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	892 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	893 </collection>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	894 </param>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	895 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	896 <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	897 <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	898 <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	899 <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	900 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	901 </conditional>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	902 <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	903 <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	904 <assert_contents>
25368452f73b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 14 diff changeset	905 <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	906 <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	907 <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	908 <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	909 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	910 </output>
13 74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	911 </test>
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	912 </tests>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	913 <help>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	914 <![CDATA[
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	915 What it does
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	916
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	917 QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	918
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	919 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 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	920
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	921 Using Quast without reference
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	922
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	923 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:
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	924
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	925 * Quast report in HTML format
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	926 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	927 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	928 * Quast log (a file technical information about Quast tool execution)
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	929
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	930 The tab delimited Quast report will contain the following information::
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	931
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	932 Assembly pit_fna cef_fna car_fna
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	933 # contigs (>= 0 bp) 100 91 94
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	934 # contigs (>= 1000 bp) 62 58 61
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	935 Total length (>= 0 bp) 6480635 6481216 6480271
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	936 Total length (>= 1000 bp) 6466917 6468946 6467103
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	937 # contigs 71 66 70
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	938 Largest contig 848753 848766 662053
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	939 Total length 6473173 6474698 6473810
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	940 GC (%) 66.33 66.33 66.33
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	941 N50 270269 289027 254671
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	942 N75 136321 136321 146521
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	943 L50 7 7 8
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	944 L75 15 15 16
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	945 # N's per 100 kbp 0.00 0.00 0.00
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	946
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	947 where values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	948
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	949 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:
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	950
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	951 .. image:: $PATH_TO_IMAGES/contig_view_noR.png
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	952 :width: 558
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	953 :height: 412
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	954
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	955 Also see `Plot description <http://quast.sourceforge.net/docs/manual.html#sec2>`_ section of the manual.
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	956
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	957 Using Quast with reference
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	958
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	959 Car, pit, and cef are in fact assemblies of Pseudomonas aeruginosa UCBPP-PA14, so we can use its genome as a reference (by supplying a Fasta file containing P. aeruginosa pa14 genome to Reference genome input box). The following outputs will be produced (note the alignment viewer):
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	960
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	961 * Quast report in HTML format
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	962 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	963 * `Alignment viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	964 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	965 * Summary of `misassemblies <http://quast.sourceforge.net/docs/manual.html#sec3.1.2>`_
4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	966 * Summary of `unaligned contigs <http://quast.sourceforge.net/docs/manual.html#sec3.1.3>`_
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	967 * Quast log (a file technical information about Quast tool execution)
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	968
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	969 With the reference Quast produces a much more comprehensive set of results::
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	970
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	971 Assembly pit_fna cef_fna car_fna
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	972 # contigs (>= 0 bp) 100 91 94
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	973 # contigs (>= 1000 bp) 62 58 61
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	974 Total length (>= 0 bp) 6480635 6481216 6480271
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	975 Total length (>= 1000 bp) 6466917 6468946 6467103
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	976 # contigs 71 66 70
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	977 Largest contig 848753 848766 662053
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	978 Total length 6473173 6474698 6473810
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	979 Reference length 6537648 6537648 6537648
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	980 GC (%) 66.33 66.33 66.33
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	981 Reference GC (%) 66.29 66.29 66.29
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	982 N50 270269 289027 254671
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	983 NG50 270269 289027 254671
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	984 N75 136321 136321 146521
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	985 NG75 136321 136321 136321
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	986 L50 7 7 8
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	987 LG50 7 7 8
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	988 L75 15 15 16
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	989 LG75 15 15 17
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	990 # misassemblies 0 0 0
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	991 # misassembled contigs 0 0 0
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	992 Misassembled contigs length 0 0 0
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	993 # local misassemblies 1 1 2
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	994 # unaligned mis. contigs 0 0 0
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	995 # unaligned contigs 0 + 0 0 + 0 0 + 0
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	996 part part part
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	997 Unaligned length 0 0 0
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	998 Genome fraction (%) 99.015 99.038 99.025
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	999 Duplication ratio 1.000 1.000 1.000
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1000 # N's per 100 kbp 0.00 0.00 0.00
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1001 # mismatches per 100 kbp 3.82 3.63 3.49
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1002 # indels per 100 kbp 1.19 1.13 1.13
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1003 Largest alignment 848753 848766 662053
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1004 Total aligned length 6473163 6474660 6473792
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1005 NA50 270269 289027 254671
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1006 NGA50 270269 289027 254671
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1007 NA75 136321 136321 146521
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1008 NGA75 136321 136321 136321
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1009 LA50 7 7 8
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1010 LGA50 7 7 8
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1011 LA75 15 15 16
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1012 LGA75 15 15 17
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1013
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1014 where, again, values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_. You can see that this report includes a variety of data that can only be computer against a reference assembly.
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1015
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	1016 Using reference also produces an Alignment viewer:
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1017
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1018 .. image:: $PATH_TO_IMAGES/Align_view.png
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1019 :width: 515
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1020 :height: 395
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1021
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1022 Alignment viewer highlights regions of interest as, in this case, missassemblies that can potentially point to genome rearrangements (see more `here <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_).
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1023
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1024 ]]>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1025 </help>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	1026 <expand macro="citations"/>
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1027 </tool>

Mercurial > repos > iuc > quast

annotate quast.xml @ 15:25368452f73b draft