quast: quast.xml annotate

annotate quast.xml @ 14:459ceb2ff536 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"

author	iuc
date	Fri, 25 Mar 2022 17:36:16 +0000
parents	74be236ac5fd
children	25368452f73b

rev	line source
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	1 <tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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])
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 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'
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	29 #set $temp_ref_list_fp = 'temp_ref_list_fp'
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	30 #set $temp_ref_list_f = open($temp_ref_list_fp, 'w')
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	31 #silent $temp_ref_list_f.write('\n'.join([x.strip() for x in $assembly.ref.references_list.split(',')]))
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	32 #silent $temp_ref_list_f.close()
5 844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	33 #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	34
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	35 #if $assembly.type == 'genome'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	36 quast
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	37 #else
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	38 metaquast
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	39 #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	40
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	41 #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	42 #for $read in $reads.input_1
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	43 --single '$read'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	44 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	45 #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	46 #for $read in $reads.input_1
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	47 --pe1 '$read'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	48 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	49 #for $read in $reads.input_2
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	50 --pe2 '$read'
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	51 #end for
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	52 #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	53 #for $read in $reads.input_1
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	54 --pe12 '$read'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	55 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	56 #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	57 #for $read in $reads.input_1
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	58 --mp1 '$read'
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 #for $read in $reads.input_2
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	61 --mp2 '$read'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	62 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	63 #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	64 #for $read in $reads.input_1
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	65 --pacbio '$read'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	66 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	67 #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	68 #for $read in $reads.input_1
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	69 --nanopore '$read'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	70 #end for
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	71 #end if
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	72
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	73 --labels '$labels'
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	74 -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	75
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	76 #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	77 #if $assembly.ref.use_ref == 'true'
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	78 -r '$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	79 #if $assembly.ref.features
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	80 --features '$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	81 #end if
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	82 #if $assembly.ref.operons
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	83 --operons '$assembly.ref.operons'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	84 #end if
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	85 $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	86 $assembly.ref.k_mer.k_mer_stats
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	87 #if str($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	88 --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	89 #end if
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	90 #else if $assembly.ref.est_ref_size
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	91 --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	92 #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	93 $assembly.orga_type
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	94 #else
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	95 #if $assembly.ref.origin == 'history'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	96 -r '$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	97 #else if $assembly.ref.origin == 'list'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	98 --references-list '$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	99 #else if $assembly.ref.origin == 'silva'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	100 --test-no-ref
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	101 --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	102 #end if
844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	103 #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	104
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	105 --min-contig $min_contig
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	106 $split_scaffolds
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	107 $large
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	108
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	109 #if str($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	110 $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	111 #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	112 #set $gene_threshold = ','.join([x.strip() for x in str($genes.gene_finding.gene_thresholds).split(',')])
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	113 --gene-thresholds '$gene_threshold'
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	114 #end if
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	115 #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	116
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	117 $genes.rna_finding
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	118 $genes.conserved_genes_finding
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	119 $alignments.use_all_alignments
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	120 --min-alignment $alignments.min_alignment
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	121 --min-identity $alignments.min_identity
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	122 --ambiguity-usage '$alignments.ambiguity_usage'
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	123 --ambiguity-score $alignments.ambiguity_score
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	124 $alignments.fragmented
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	125 $alignments.upper_bound_assembly
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	126 #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	127 --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	128 #end if
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	129
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	130 #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	131 #if $advanced.fragmented_max_indent != ''
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	132 --fragmented-max-indent $advanced.fragmented_max_indent
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	133 #end if
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	134 #end if
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	135
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	136 #set $contig_thresholds = ','.join([x.strip() for x in str($advanced.contig_thresholds).split(',')])
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	137 --contig-thresholds '$contig_thresholds'
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	138 $advanced.strict_NA
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	139 --extensive-mis-size $advanced.extensive_mis_size
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	140 --scaffold-gap-max-size $advanced.scaffold_gap_max_size
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	141 --unaligned-part-size $advanced.unaligned_part_size
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	142 $advanced.skip_unaligned_mis_contigs
3 1dd49661494f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67 iuc parents: 2 diff changeset	143
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	144 #if str($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	145 #for $k in $in.inputs
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	146 '$k'
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	147 #end for
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	148 #else
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	149 #for $k in $in.inputs
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	150 '$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	151 #end for
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	152 #end if
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	153
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	154 --threads \${GALAXY_SLOTS:-1}
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	155
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	156 && mkdir -p '$report_html.files_path'
5 844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	157 && cp outputdir/*.html '$report_html.files_path'
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	158
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	159 #if ($assembly.type == 'genome' and $assembly.ref.use_ref) or ($assembly.type == 'metagenome' and $assembly.ref.origin != 'none')
5 844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	160 && cp -R outputdir/icarus_viewers '$report_html.files_path'
844452fe09f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	161 #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	162
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	163 #if $assembly.type == 'metagenome'
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	164 && if [[ -d "outputdir/combined_reference/" ]]; then mkdir -p '$report_html_meta.files_path' && cp outputdir/combined_reference/*.html '$report_html_meta.files_path'; fi
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	165 #if $assembly.ref.origin != 'none'
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	166 && if [[ -d "outputdir/combined_reference/" ]]; then cp -R outputdir/combined_reference/icarus_viewers '$report_html_meta.files_path'; fi
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	167 && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '$krona.files_path' && cp outputdir/krona_charts/*.html '$krona.files_path'; fi
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	168 #end if
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	169 #end if
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	170
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	171 ]]>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	172 </command>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	173 <inputs>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	174 <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	175 <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	176 <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	177 <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	178 </param>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	179 <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	180 <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	181 <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	182 <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	183 </repeat>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	184 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	185 <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	186 <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	187 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	188 </conditional>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	189 <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	190 <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	191 <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	192 <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	193 <option value="paired">Illumina 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	194 <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	195 <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	196 <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	197 <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	198 </param>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	199 <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	200 <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	201 <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	202 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	203 <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	204 <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	205 <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	206 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	207
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	208 <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	209 <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	210 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	211 <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	212 <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	213 <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	214 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	215 <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	216 <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	217 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	218 <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	219 <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	220 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	221 </conditional>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	222 <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	223 <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	224 <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	225 <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	226 </param>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	227 <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	228 <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	229 <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	230 <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	231 <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	232 </param>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	233 <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	234 <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	235 <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	236 <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	237 <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	238 <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	239 <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	240 <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	241 </param>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	242 <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	243 <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	244 </when>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	245 <when value=""/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	246 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	247 <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	248 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	249 <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	250 <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	251 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	252 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	253 <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	254 <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	255 <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	256 <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	257 </param>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	258 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	259 <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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <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	266 </param>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	267 <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	268 <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	269 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	270 <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	271 <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	272 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	273 <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	274 <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	275 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	276 <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	277 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	278 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	279 </conditional>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	280 <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	281 <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	282 <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	283 <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	284 <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	285 <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	286 <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	287 <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	288 <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	289 <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	290 </param>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	291 <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	292 <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	293 <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	294 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	295 <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	296 <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	297 <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	298 </when>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	299 </conditional>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	300 <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	301 <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	302 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	303 <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	304 <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	305 <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	306 <param argument="--min-identity" type="float" value="95.0" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. ote that all alignments with IDY% less than 80.0% will be filtered regardless of this threshold. "/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	307 <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	308 <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	309 <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	310 <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	311 </param>
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="--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	313 <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	314 <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	315 <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)"/>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	316 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	317 <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	318 <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	319 <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	320 <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	321 <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	322 <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	323 <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	324 <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" />
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	325 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <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	333 </param>
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	334 </inputs>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	335 <outputs>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	336 <data name="report_tabular" format="tabular" label="${tool.name} on ${on_string}: tabular report" from_work_dir="outputdir/report.tsv">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	337 <filter>assembly['type'] == 'genome' and 'tabular' in output_files</filter>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	338 </data>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	339 <data name="report_tabular_meta" format="tabular" label="${tool.name} on ${on_string}: tabular report for combined reference genome" from_work_dir="outputdir/combined_reference/report.tsv">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	340 <filter>assembly['type'] == 'metagenome' and 'tabular' in output_files</filter>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	341 </data>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	342 <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html">
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	343 <filter>'html' in output_files</filter>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	344 </data>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	345 <data name="report_html_meta" format="html" label="${tool.name} on ${on_string}: HTML report for combined reference genome" from_work_dir="outputdir/combined_reference/report.html">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	346 <filter>assembly['type'] == 'metagenome' and 'html' in output_files</filter>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	347 </data>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	348 <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF report" from_work_dir="outputdir/report.pdf">
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	349 <filter>assembly['type'] == 'genome' and 'pdf' in output_files</filter>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	350 </data>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	351 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log">
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	352 <filter>assembly['type'] == 'genome' and 'log' in output_files</filter>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	353 </data>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	354 <data name="log_meta" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/metaquast.log">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	355 <filter>assembly['type'] == 'metagenome' and 'log' in output_files</filter>
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	356 </data>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	357 <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies report" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	358 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	359 <filter>'tabular' in output_files</filter>
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	360 </data>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	361 <data name="unalign" format="tabular" label="${tool.name} on ${on_string}: Unaligned contigs report" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	362 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	363 <filter>'tabular' in output_files</filter>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	364 </data>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	365 <data name="kmers" format="tabular" label="${tool.name} on ${on_string}: K-mer-based metrics report" from_work_dir="outputdir/k_mer_stats/kmers_report.txt">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	366 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['k_mer']['k_mer_stats'] != ''</filter>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	367 <filter>'tabular' in output_files</filter>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	368 </data>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	369 <data name="circos_output" format="png" from_work_dir="outputdir/circos/circos.png" label="${tool.name} on ${on_string}: Circos plot">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	370 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['circos']</filter>
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	371 </data>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	372 <collection name="metrics_tabular" type="list" label="${tool.name} on ${on_string}: Tabular reports for key metrics" >
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	373 <discover_datasets pattern="(?P<designation>.+).tsv" directory="outputdir/summary/TSV/" format="tabular"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	374 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	375 </collection>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	376 <collection name="metrics_pdf" type="list" label="${tool.name} on ${on_string}: PDF reports for key metrics" >
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	377 <discover_datasets pattern="(?P<designation>.+).pdf" directory="outputdir/summary/PDF/" format="pdf"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	378 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	379 </collection>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	380 <data name="krona" format="html" label="${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	381 <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	382 </data>
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	383 </outputs>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	384 <tests>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	385 <!-- 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	386 <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	387 <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	388 <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	389 <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	390 <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	391 <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	392 </repeat>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	393 <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	394 <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	395 <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	396 </repeat>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	397 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	398 <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	399 <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	400 <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	401 <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	402 <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	403 <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	404 <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	405 <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	406 <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	407 <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	408 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	409 <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	410 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	411 <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	412 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	413 <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	414 <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	415 <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	416 <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	417 <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	418 <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	419 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	420 <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	421 <param name="conserved_genes_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	422 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	423 <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	424 <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	425 <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	426 <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	427 <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	428 <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	429 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	430 <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	431 <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	432 <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	433 <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	434 <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	435 <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	436 <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	437 <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	438 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	439 <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	440 <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	441 <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	442 </test>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	443 <!-- 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	444 <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	445 <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	446 <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	447 <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	448 <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	449 <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	450 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	451 <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	452 <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	453 <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	454 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	455 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	456 <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	457 <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	458 <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	459 <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	460 <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	461 <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	462 <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	463 <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	464 <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	465 <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	466 </conditional>
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="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	468 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	469 </conditional>
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="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	471 <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	472 <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	473 <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	474 <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	475 <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	476 <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	477 <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	478 <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	479 </test>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	480 <!-- 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	481 <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	482 <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	483 <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	484 <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	485 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	486 <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	487 <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	488 <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	489 <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	490 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	491 <param name="orga_type" value="--eukaryote"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	492 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	493 <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	494 <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	495 <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	496 <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	497 <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	498 <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	499 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	500 <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	501 <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	502 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	503 <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	504 <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	505 <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	506 <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	507 <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	508 <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	509 <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	510 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	511 <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	512 <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	513 <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	514 <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	515 <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	516 <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	517 <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	518 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	519 <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	520 <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	521 <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	522 <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	523 </test>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	524 <!-- Test 04: metagenomics -->
6 bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	525 <test>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	526 <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	527 <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	528 <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	529 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	530 <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	531 <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	532 <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	533 <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	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 </conditional>
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="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	537 <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	538 <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	539 <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	540 <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	541 <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	542 </conditional>
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="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	544 <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	545 </section>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	546 <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	547 <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	548 <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	549 <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	550 <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	551 <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	552 <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	553 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	554 <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	555 <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	556 <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	557 <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	558 <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	559 <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	560 <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	561 </section>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	562 <param name="output_files" value="log"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	563 <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	564 <assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	565 <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	566 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	567 </output>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	568 </test>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	569 <!-- 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	570 <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	571 <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	572 <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	573 <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	574 <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	575 <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	576 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	577 <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	578 <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	579 <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	580 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	581 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	582 <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	583 <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	584 <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	585 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	586 <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	587 <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	588 <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	589 <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	590 <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	591 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	592 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	593 <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	594 <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	595 <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	596 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	597 <param name="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	598 <output name="report_tabular" file="test5.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	599 <output name="mis_ass" file="test5_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	600 <output name="unalign" file="test5_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	601 </test>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	602 <!-- 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	603 <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	604 <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	605 <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	606 <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	607 <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	608 <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	609 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	610 <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	611 <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	612 <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	613 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	614 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	615 <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	616 <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	617 <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	618 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	619 <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	620 <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	621 </test>
14 459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	622 <!-- 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	623 <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	624 <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	625 <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	626 <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	627 <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	628 <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	629 </repeat>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	630 <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	631 <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	632 <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	633 </repeat>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	634 </conditional>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	635 <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	636 <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	637 <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	638 </conditional>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	639 <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	640 <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	641 </test>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	642 <!-- 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	643 <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	644 <conditional name="in">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	645 <param name="custom" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	646 <param name="inputs" value="test8.fasta"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	647 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	648 <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	649 <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	650 <conditional name="ref">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	651 <param name="origin" value="none"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	652 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	653 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	654 <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	655 <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	656 <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	657 <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	658 <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	659 <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	660 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	661 <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	662 <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	663 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	664 <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	665 <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	666 <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	667 <param name="min_identity" value="95.0"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	668 <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	669 <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	670 <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	671 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	672 <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	673 <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	674 <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	675 <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	676 <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	677 <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	678 <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	679 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	680 <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	681 <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	682 <assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	683 <has_text text="contigs (>= 0 bp)" />
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	684 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	685 </output>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	686 <output_collection name="metrics_tabular" type="list" count="14"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	687 <output_collection name="metrics_pdf" type="list" count="15"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	688 </test>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	689 <!-- Test 09: metagenomics log, html and krona outputs-->
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	690 <test expect_num_outputs="4">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	691 <conditional name="in">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	692 <param name="custom" value="false"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	693 <param name="inputs" value="test8.fasta"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	694 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	695 <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	696 <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	697 <conditional name="ref">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	698 <param name="origin" value="none"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	699 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	700 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	701 <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	702 <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	703 <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	704 <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	705 <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	706 <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	707 </conditional>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	708 <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	709 <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	710 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	711 <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	712 <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	713 <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	714 <param name="min_identity" value="95.0"/>
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="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	716 <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	717 <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	718 </section>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	719 <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	720 <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	721 <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	722 <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	723 <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	724 <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	725 <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	726 </section>
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="output_files" value="html,log,krona"/>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	728 <output name="report_html" ftype="html">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	729 <assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	730 <has_text text="Vibrio_parahaemolyticus" />
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	731 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	732 </output>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	733 <output name="report_html_meta" ftype="html">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	734 <assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	735 <has_text text="Total length (>= 1000 bp)" />
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	736 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	737 </output>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	738 <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	739 <assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	740 <has_text text="Vibrio_parahaemolyticus \| successfully downloaded" />
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	741 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	742 </output>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	743 <output name="krona" ftype="html">
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	744 <assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	745 <has_text text="Vibrio_parahaemolyticus" />
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	746 </assert_contents>
459ceb2ff536 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 13 diff changeset	747 </output>
13 74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 12 diff changeset	748 </test>
0 350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	749 </tests>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	750 <help>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	751 <![CDATA[
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	752 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	753
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	754 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	755
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	756 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	757
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	758 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	759
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	760 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	761
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	762 * 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	763 * `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	764 * `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	765 * 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	766
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	767 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	768
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	769 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	770 # 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	771 # 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	772 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	773 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	774 # 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	775 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	776 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	777 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	778 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	779 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	780 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	781 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	782 # 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	783
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	784 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	785
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	786 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	787
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	788 .. 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	789 :width: 558
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	790 :height: 412
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	791
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	792 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	793
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	794 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	795
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	796 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	797
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	798 * 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	799 * `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	800 * `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	801 * `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	802 * 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	803 * 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	804 * 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	805
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	806 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	807
4 d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	808 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	809 # 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	810 # 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	811 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	812 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	813 # 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	814 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	815 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	816 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	817 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	818 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	819 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	820 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	821 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	822 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	823 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	824 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	825 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	826 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	827 # 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	828 # 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	829 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	830 # 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	831 # 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	832 # 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	833 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	834 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	835 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	836 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	837 # 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	838 # 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	839 # 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	840 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	841 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	842 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	843 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	844 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	845 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	846 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	847 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	848 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	849 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	850
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	851 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	852
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	853 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	854
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	855 .. 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	856 :width: 515
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	857 :height: 395
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	858
8 4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	859 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	860
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	861 ]]>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	862 </help>
10 e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 9 diff changeset	863 <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	864 </tool>

Mercurial > repos > iuc > quast

annotate quast.xml @ 14:459ceb2ff536 draft