quast: quast.xml annotate

annotate quast.xml @ 15:72472698a2df draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69

author	iuc
date	Thu, 02 Mar 2023 10:38:54 +0000
parents	3061c8b029e5
children

rev	line source
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1 <tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0 736d51130b41 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 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	3 <macros>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	4 <import>macros.xml</import>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	5 </macros>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	6 <expand macro="bio_tools"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	7 <expand macro='requirements' />
5 81df4950d65b 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 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	9 <![CDATA[
5 81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	10 #import re
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	11 #import os
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	12
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	13 #if str($mode.in.custom) == 'false'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	14 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	15 #set $labels = re.sub('[^\w\-_]', '_', str($mode.in.inputs.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	16 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	17 #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $mode.in.inputs])
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	18 #end if
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	19 echo $labels &&
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	20 #else
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	21 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	22 #if str($mode.in.labels) != ''
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	23 #set $labels = re.sub('[^\w\-_]', '_', str($mode.in.labels))
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	24 #else
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	25 #set $labels = re.sub('[^\w\-_]', '_', str($mode.in.input.element_identifier))
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	26 #end if
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	27 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	28 #set $labels = []
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	29 #for $x in $mode.in.inputs
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	30 #if str($x.labels) != ''
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	31 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels)))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	32 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	33 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.input.element_identifier)))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	34 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	35 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	36 #set $labels = ','.join($labels)
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	37 #end if
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	38 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	39
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	40 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list'
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	41 #set $temp_ref_list_fp = 'temp_ref_list'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	42 #for $i in $assembly.ref.references_list.split(',')
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	43 echo $i >> $temp_ref_list_fp &&
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	44 #end for
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	45 #end if
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	46
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	47 #if $mode.reads.reads_option == 'paired'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	48 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	49 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	50 ln -s '$mode.reads.input_1' 'pe1-${identifier}.${mode.reads.input_1.ext}' &&
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	51 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_2.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	52 ln -s '$mode.reads.input_2' 'pe2-${identifier}.${mode.reads.input_2.ext}' &&
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	53 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	54 #for $read in $mode.reads.input_1
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	55 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	56 ln -s '$read' 'pe1-${identifier}.${read.ext}' &&
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	57 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	58 #for $read in $mode.reads.input_2
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	59 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	60 ln -s '$read' 'pe2-${identifier}.${read.ext}' &&
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	61 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	62 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	63 #else if $mode.reads.reads_option == 'paired_collection'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	64 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	65 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	66 ln -s '$mode.reads.input_1.forward' 'pe1-${identifier}.${mode.reads.input_1.forward.ext}' &&
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	67 ln -s '$mode.reads.input_1.reverse' 'pe2-${identifier}.${mode.reads.input_1.reverse.ext}' &&
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	68 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	69 #for $read in $mode.reads.input_1
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	70 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	71 ln -s '$read.forward' 'pe1-${identifier}.${read.forward.ext}' &&
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	72 ln -s '$read.reverse' 'pe2-${identifier}.${read.reverse.ext}' &&
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	73 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	74 #end if
5 81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	75 #end if
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	76
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	77 #if $assembly.type == 'genome'
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	78 quast
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	79 #else
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	80 metaquast
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	81 #end if
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	82
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	83 #if $mode.reads.reads_option == 'single'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	84 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	85 --single '$mode.reads.input_1'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	86 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	87 #for $read in $mode.reads.input_1
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	88 --single '$read'
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	89 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	90 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	91 #else if $mode.reads.reads_option == 'paired'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	92 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	93 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	94 --pe1 'pe1-${identifier}.${mode.reads.input_1.ext}'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	95 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_2.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	96 --pe2 'pe2-${identifier}.${mode.reads.input_2.ext}'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	97 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	98 #for $read in $mode.reads.input_1
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	99 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	100 --pe1 'pe1-${identifier}.${read.ext}'
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	101 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	102 #for $read in $mode.reads.input_2
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	103 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	104 --pe2 'pe2-${identifier}.${read.ext}'
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	105 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	106 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	107 #else if $mode.reads.reads_option == 'paired_collection'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	108 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	109 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	110 --pe1 'pe1-${identifier}.${mode.reads.input_1.forward.ext}'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	111 --pe2 'pe2-${identifier}.${mode.reads.input_1.reverse.ext}'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	112 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	113 #for $read in $mode.reads.input_1
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	114 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	115 --pe1 'pe1-${identifier}.${read.forward.ext}'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	116 --pe2 'pe2-${identifier}.${read.reverse.ext}'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	117 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	118 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	119 #else if $mode.reads.reads_option == 'paired_interlaced'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	120 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	121 --pe12 '$mode.reads.input_1'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	122 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	123 #for $read in $mode.reads.input_1
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	124 --pe12 '$read'
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	125 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	126 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	127 #else if $mode.reads.reads_option == 'mate_paired'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	128 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	129 --mp1 '$mode.reads.input_1'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	130 --mp2 '$mode.reads.input_2'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	131 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	132 #for $read in $mode.reads.input_1
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	133 --mp1 '$read'
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	134 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	135 #for $read in $mode.reads.input_2
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	136 --mp2 '$read'
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	137 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	138 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	139 #else if $mode.reads.reads_option == 'pacbio'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	140 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	141 --pacbio '$mode.reads.input_1'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	142 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	143 #for $read in $mode.reads.input_1
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	144 --pacbio '$read'
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	145 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	146 #end if
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	147 #else if $mode.reads.reads_option == 'nanopore'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	148 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	149 --nanopore '$mode.reads.input_1'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	150 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	151 #for $read in $mode.reads.input_1
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	152 --nanopore '$read'
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	153 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	154 #end if
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	155 #end if
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	156 --labels '$labels'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	157 -o 'outputdir'
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	158
f30d03867854 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'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	160 #if $assembly.ref.use_ref == 'true'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	161 -r '$assembly.ref.r'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	162 #if $assembly.ref.features
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	163 --features '$assembly.ref.features'
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	164 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	165 #if $assembly.ref.operons
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	166 --operons '$assembly.ref.operons'
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	167 #end if
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	168 $assembly.ref.circos
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	169 $assembly.ref.k_mer.k_mer_stats
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	170 #if str($assembly.ref.k_mer.k_mer_stats) != ''
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	171 --k-mer-size $assembly.ref.k_mer.k_mer_size
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	172 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	173 #else if $assembly.ref.est_ref_size
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	174 --est-ref-size $assembly.ref.est_ref_size
5 81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	175 #end if
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	176 $assembly.orga_type
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	177 #else if $assembly.type == 'metagenome'
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	178 #if $assembly.ref.origin == 'history'
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	179 -r '$assembly.ref.r'
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	180 #else if $assembly.ref.origin == 'list'
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	181 --references-list '$temp_ref_list_fp'
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	182 #else if $assembly.ref.origin == 'silva'
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	183 --max-ref-num $assembly.ref.max_ref_num
5 81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	184 #end if
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	185 $assembly.reuse_combined_alignments
5 81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	186 #end if
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	187 --min-identity $assembly.min_identity
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	188 --min-contig $min_contig
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	189 $split_scaffolds
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	190 $large
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	191
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	192 #if str($genes.gene_finding.tool) != 'none'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	193 $genes.gene_finding.tool
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	194 #if $genes.gene_finding.tool == '--gene_finding' or $genes.gene_finding.tool == '--glimmer'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	195 #set $gene_threshold = ','.join([x.strip() for x in str($genes.gene_finding.gene_thresholds).split(',')])
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	196 --gene-thresholds '$gene_threshold'
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	197 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	198 #end if
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	199
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	200 $genes.rna_finding
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	201 $genes.conserved_genes_finding
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	202 $alignments.use_all_alignments
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	203 --min-alignment $alignments.min_alignment
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	204 --ambiguity-usage '$alignments.ambiguity_usage'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	205 --ambiguity-score $alignments.ambiguity_score
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	206 $alignments.fragmented
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	207 $alignments.upper_bound_assembly
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	208 #if $alignments.upper_bound_min_con
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	209 --upper-bound-min-con $alignments.upper_bound_min_con
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	210 #end if
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	211 #if $alignments.local_mis_size
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	212 --local-mis-size $alignments.local_mis_size
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	213 #end if
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	214
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	215 #if $alignments.fragmented
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	216 #if $advanced.fragmented_max_indent != ''
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	217 --fragmented-max-indent $advanced.fragmented_max_indent
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	218 #end if
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	219 #end if
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	220
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	221 #set $contig_thresholds = ','.join([x.strip() for x in str($advanced.contig_thresholds).split(',')])
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	222 --contig-thresholds '$contig_thresholds'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	223 $advanced.strict_NA
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	224 --extensive-mis-size $advanced.extensive_mis_size
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	225 --scaffold-gap-max-size $advanced.scaffold_gap_max_size
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	226 --unaligned-part-size $advanced.unaligned_part_size
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	227 $advanced.skip_unaligned_mis_contigs
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	228 $advanced.report_all_metrics
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	229 --x-for-Nx $advanced.x_for_Nx
3 6fcbee531de6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67 iuc parents: 2 diff changeset	230
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	231 #if str($mode.in.custom) == 'false'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	232 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	233 '$mode.in.inputs'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	234 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	235 #for $k in $mode.in.inputs
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	236 '$k'
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	237 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	238 #end if
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	239 #else
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	240 #if $mode.mode == 'individual'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	241 '$mode.in.input'
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	242 #else
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	243 #for $k in $mode.in.inputs
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	244 '$k.input'
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	245 #end for
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	246 #end if
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	247 #end if
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	248 --threads \${GALAXY_SLOTS:-1}
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	249
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	250 #if $assembly.type == 'genome'
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	251 && mkdir -p '$report_html.files_path'
5 81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	252 && cp outputdir/*.html '$report_html.files_path'
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	253 #if $assembly.ref.use_ref
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	254 && cp -R outputdir/icarus_viewers '$report_html.files_path'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	255 #end if
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	256 #else
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	257 && if [[ -f "outputdir/report.tsv" ]]; then mkdir -p "outputdir/combined_reference/" && cp "outputdir/report.tsv" "outputdir/combined_reference/report.tsv"; fi
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	258 && if [[ -f "outputdir/report.html" ]]; then mkdir -p "outputdir/combined_reference/" && cp outputdir/*.html "outputdir/combined_reference/"; fi
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	259 && mkdir -p '$report_html_meta.files_path'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	260 && cp outputdir/combined_reference/*.html '$report_html_meta.files_path'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	261 && if [[ -d "outputdir/icarus_viewers" ]]; then cp -R outputdir/icarus_viewers 'outputdir/combined_reference/'; fi
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	262 && if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '$report_html_meta.files_path'; fi
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	263 && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '$krona.files_path' && cp outputdir/krona_charts/*.html '$krona.files_path'; fi
5 81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa iuc parents: 4 diff changeset	264 #end if
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	265 ]]></command>
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	266 <inputs>
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	267 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	268 <param name="mode" type="select" label="Assembly mode?" help="Useful to know if contigs have been generated all samples together (co-assembly) or on each sample individually (individual assembly)">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	269 <option value="individual">Individual assembly (1 contig file per sample)</option>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	270 <option value="co" selected="true">Co-assembly (1 contig file for several samples)</option>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	271 </param>
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	272 <when value="individual">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	273 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	274 <expand macro="custom"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	275 <when value="true">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	276 <expand macro="labelled_input"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	277 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	278 <when value="false">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	279 <param name="inputs" type="data" format="fasta" label="Contigs/scaffolds file"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	280 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	281 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	282 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	283 <expand macro="reads_option"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	284 <when value="disabled"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	285 <when value="single">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	286 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	287 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	288 <when value="paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	289 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #1" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	290 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #2" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	291 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	292 <when value="paired_collection">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	293 <param name="input_1" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fasta,fasta.gz" label="FASTQ/FASTA files" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	294 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	295 <when value="paired_interlaced">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	296 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	297 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	298 <when value="mate_paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	299 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #1" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	300 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #2" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	301 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	302 <when value="pacbio">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	303 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	304 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	305 <when value="nanopore">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	306 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	307 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	308 </conditional>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	309 </when>
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	310 <when value="co">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	311 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	312 <expand macro="custom"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	313 <when value="true">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	314 <repeat name="inputs" title="Contigs/scaffolds" min="1">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	315 <expand macro="labelled_input"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	316 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	317 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	318 <when value="false">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	319 <param name="inputs" type="data" format="fasta" multiple="true" label="Contigs/scaffolds file"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	320 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	321 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	322 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	323 <expand macro="reads_option"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	324 <when value="disabled"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	325 <when value="single">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	326 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	327 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	328 <when value="paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	329 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	330 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	331 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	332 <when value="paired_collection">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	333 <param name="input_1" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,fasta,fasta.gz" label="FASTQ/FASTA files" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	334 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	335 <when value="paired_interlaced">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	336 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	337 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	338 <when value="mate_paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	339 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	340 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	341 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	342 <when value="pacbio">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	343 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	344 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	345 <when value="nanopore">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	346 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	347 </when>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	348 </conditional>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	349 </when>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	350 </conditional>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	351 <conditional name="assembly">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	352 <param name="type" type="select" label="Type of assembly">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	353 <option value="genome">Genome</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	354 <option value="metagenome">Metagenome</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	355 </param>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	356 <when value="genome">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	357 <conditional name="ref">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	358 <param name="use_ref" type="select" label="Use a reference genome?" help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference.">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	359 <option value="true">Yes</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	360 <option value="false" selected="true">No</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	361 </param>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	362 <when value="true">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	363 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	364 <param argument="--features" type="data" format="gff, gff3, bed" optional="true" label="Genomic feature positions in the reference genome" help="Gene coordinates for the reference genome"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	365 <param argument="--operons" type="data" format="gff, gff3, bed" optional="true" label="Operon positions in the reference genome" help="Operon coordinates for the reference genome"/>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	366 <conditional name="k_mer">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	367 <param argument="--k-mer-stats" type="select" label="Compute k-mer-based quality metrics?" help="It is recommended for large genomes. This may significantly increase memory and time consumption on large genomes">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	368 <option value="--k-mer-stats">Yes</option>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	369 <option value="" selected="true">No</option>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	370 </param>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	371 <when value="--k-mer-stats">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	372 <param argument="--k-mer-size" type="integer" value="101" label="Size of k" />
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	373 </when>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	374 <when value=""/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	375 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	376 <param argument="--circos" type="boolean" truevalue="--circos" falsevalue="" checked="false" label="Generage Circos plot" help="Plot Circos version of Icarus contig alignment viewer"/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	377 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	378 <when value="false">
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	379 <param argument="--est-ref-size" type="integer" optional="true" label="Estimated reference genome size (in bp) for computing NGx statistics" help=""/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	380 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	381 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	382 <param name="orga_type" type="select" label="Type of organism">
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	383 <option value="">Prokaryotes: use of GeneMarkS for gene finding (default)</option>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	384 <option value="--eukaryote">Eukaryote: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--eukaryote)</option>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	385 <option value="--fungus">Fungus: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--fungus)</option>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	386 </param>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	387 <expand macro="min_identity_macros" value="95"/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	388 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	389 <when value="metagenome">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	390 <conditional name="ref">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	391 <param name="origin" type="select" label="Reference genome" help="If no reference genomes is provided, the tool will try to identify genome content of the metagenome. By default, it will align contigs to SILVA 16S rRNA database, i.e. FASTA file containing small subunit ribosomal RNA sequences to identify genomes. The reference genomes for the chosen genomes are downloaded from the NCBI database. After that, Quast is run on all of them. Reference genomes with low genome fraction (less than 10%) are removed. The usual MetaQUAST analysis continues with the remaining references.">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	392 <option value="silva" selected="true">From SILVA database</option>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	393 <option value="history">From history</option>
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	394 <option value="list">From a list</option>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	395 </param>
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	396 <when value="silva">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	397 <param argument="--max-ref-num" type="integer" value="50" label="Maximum number of reference genomes (per each assembly) to download after searching in the SILVA databa" />
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	398 </when>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	399 <when value="history">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	400 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	401 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	402 <when value="list">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	403 <param argument="--references-list" type="text" value="" label="Comma-separated list of reference genomes" help="MetaQUAST will search for these references in the NCBI database and will download the found ones"/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	404 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	405 </conditional>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	406 <param argument="--reuse-combined-alignments" type="boolean" truevalue="--reuse-combined-alignments" falsevalue="" checked="false" label="Reuse the alignments on the combined reference" help="Reuse the alignments on the combined reference in the subsequent runs per separate references. That is, the alignment procedure is performed only once (for all assemblies against the combined reference) and does NOT executed for each subgroups of contigs against the corresponding separate reference genomes. In each separate reference run, all precomputed assembly alignments for other references are simply ignored" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	407 <expand macro="min_identity_macros" value="90"/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	408 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	409 </conditional>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	410 <param argument="--min-contig" type="integer" value="500" label="Lower threshold for a contig length (in bp)" help="Shorter contigs won't be taken into account"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	411 <param argument="--split-scaffolds" type="boolean" truevalue="--split-scaffolds" falsevalue="" checked="false" label="Are assemblies scaffolds rather than contigs?" help="QUAST will add split versions of assemblies to the comparison. Assemblies are split by continuous fragments of N's of length >= 10. If broken version is equal to the original assembly (i.e. nothing was split) it is not included in the comparison."/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	412 <param argument="--large" type="boolean" truevalue="--large" falsevalue="" checked="false" label="Is genome large (> 100 Mbp)?" help="Use optimal parameters for evaluation of large genomes. Affects speed and accuracy. In particular, imposes --eukaryote --min-contig 3000 --min-alignment 500 --extensive-mis-size 7000 (can be overridden manually with the corresponding options). In addition, this mode tries to identify misassemblies caused by transposable elements and exclude them from the number of misassemblies."/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	413 <section name="genes" title="Genes">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	414 <conditional name="gene_finding">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	415 <param name="tool" type="select" label="Tool for gene prediction" help="">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	416 <option value="none">Don't predict genes</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	417 <option value="--gene-finding">GeneMarkS if prokaryotes or GeneMark-ES if eukaryotes or fungi</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	418 <option value="--mgm">MetaGeneMark, specially for metagenomic assembly</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	419 <option value="--glimmer">Glimmer</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	420 </param>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	421 <when value="none"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	422 <when value="--gene-finding">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	423 <expand macro="gene_thresholds"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	424 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	425 <when value="--mgm"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	426 <when value="--glimmer">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	427 <expand macro="gene_thresholds"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	428 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	429 </conditional>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	430 <param argument="--rna-finding" type="boolean" truevalue="--rna-finding" falsevalue="" checked="false" label="Enables ribosomal RNA gene finding?" help="By default, we assume that the genome is prokaryotic, and Barrnap uses the bacterial database for rRNA prediction. If the genome is eukaryotic (fungal), use --eukaryote (--fungus) option to force Barrnap to work with the eukaryotic (fungal) database. "/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	431 <param argument="--conserved-genes-finding" type="boolean" truevalue="--conserved-genes-finding" falsevalue="" checked="false" label="Enables search for Universal Single-Copy Orthologs using BUSCO?" help="By default, we assume that the genome is prokaryotic, and BUSCO uses the bacterial database of orthologs. If the genome is eukaryotic (fungal), use --eukaryote (--fungus) option to force BUSCO to work with the eukaryotic (fungal) database. "/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	432 </section>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	433 <section name="alignments" title="Alignments">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	434 <param argument="--use-all-alignments" type="boolean" truevalue="--use-all-alignments" falsevalue="" checked="false" label="Use all alignments as in QUAST v.1.*. to compute genome fraction, # genomic features, # operons metrics?" help="By default, QUAST v.2.0 and higher filters out ambiguous and redundant alignments, keeping only one alignment per contig (or one set of non-overlapping or slightly overlapping alignments)"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	435 <param argument="--min-alignment" type="integer" value="65" label="Minimum length of alignment" help="Alignments shorter than this value will be filtered. Note that all alignments shorter than 65 bp will be filtered regardless of this threshold."/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	436 <param argument="--ambiguity-usage" type="select" label="How processing equally good alignments of a contig (probably repeats)?" help="">
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	437 <option value="none">Skip all such alignments</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	438 <option value="one" selected="true">Take only one (the very best one)</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	439 <option value="all">Use all alignments. It can cause a significant increase of # mismatches (repeats are almost always inexact due to accumulated SNPs, indels, etc.). It is useful for metagenomic assemblies where ambiguous alignments might represent homologous sequences of different strains</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	440 </param>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	441 <param argument="--ambiguity-score" type="float" value="0.99" min="0.8" max="1.0" label="Score S for defining equally good alignments of a single contig" help="All alignments are sorted by decreasing LEN × IDY% value. All alignments with LEN × IDY% less than S × best(LEN × IDY%) are discarded. "/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	442 <param argument="--fragmented" type="boolean" truevalue="--fragmented" falsevalue="" checked="false" label="Fragmented reference genome" help="Reference genome is fragmented (e.g. a scaffold reference). QUAST will try to detect misassemblies caused by the fragmentation and mark them fake (will be excluded from misassemblies). Note: QUAST will not detect misassemblies caused by the linear representation of circular genome "/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	443 <param argument="--upper-bound-assembly" type="boolean" truevalue="--upper-bound-assembly" falsevalue="" label="Simulate upper bound assembly" help="Simulate upper bound assembly based on the reference genome and a given set reads (mate-pairs or long reads, such as Pacbio SMRT/Oxford Nanopore, are REQUIRED). This assembly is added to the comparison and could be useful for estimating the upper bounds of completeness and contiguity that theoretically can be reached by assembly software from this particular set of reads. The concept is based on the fact that the reference genome cannot be completely reconstructed from raw reads due to long genomic repeats and low covered regions." />
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	444 <param argument="--upper-bound-min-con" type="integer" value="" optional="true" label="Minimal number of 'connecting reads' needed for joining upper bound contigs into a scaffold" help="This is important for a realistic estimation of genome assembly fragmentation due to long repeats. The default values is 2 for mate-pairs and 1 for long reads (PacBio or Nanopore libraries)"/>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	445 <param argument="--local-mis-size" type="integer" value="200" optional="true" label="Minimal local misassembly size" help="Lower threshold for the local misassembly size. Shorter inconsistencies are considered as (long) indels. The default value is 200 bp. Note that the threshold should be equal to or lower than minimal extensive misassembly size, which is 1000 bp by default"/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	446 </section>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	447 <section name="advanced" title="Advanced options">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	448 <param argument="--contig-thresholds" type="text" value="0,1000" label="Comma-separated list of contig length thresholds (in bp)" help="Used in # contigs ≥ x and total length (≥ x) metrics"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	449 <param argument="--strict-NA" type="boolean" truevalue="--strict-NA" falsevalue="" checked="false" label="Break contigs at every misassembly event (including local ones) to compute NAx and NGAx statistics?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	450 <param argument="--extensive-mis-size" type="integer" value="1000" min="85" label="Lower threshold for the relocation size (gap or overlap size between left and right flanking sequence)" help="Shorter relocations are considered as local misassemblies. It does not affect other types of extensive misassemblies (inversions and translocations). The default value is 1000 bp. Note that the threshold should be greater than maximum indel length which is 85 bp."/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	451 <param argument="--scaffold-gap-max-size" type="integer" value="1000" label="Max allowed scaffold gap length difference for detecting corresponding type of misassemblies" help="Longer inconsistencies are considered as relocations and thus, counted as extensive misassemblies. The default value is 10000 bp. Note that the threshold make sense only if it is greater than extensive misassembly size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	452 <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	453 <param argument="--skip-unaligned-mis-contigs" type="boolean" truevalue="" falsevalue="--skip-unaligned-mis-contigs" checked="true" label="Distinguish contigs with more than 50% unaligned bases as a separate group of contigs?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	454 <param argument="--fragmented-max-indent" type="integer" min="0" value="" optional="true" label="Fragment max indent" help="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments. The value should be less than extensive misassembly size.Default value is 50. Note: requires --fragmented option" />
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	455 <param argument="--report-all-metrics" type="boolean" truevalue="--report-all-metrics" falsevalue="" checked="false" label="Report all metrics" help="Keep all quality metrics in the main report. Usually, all not-relevant metrics are not included in the report, e.g., reference-based metrics in the no-reference mode. Also, if metric values are undefined for all input assemblies, the metric is removed from the report" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	456 <param argument="--x-for-Nx" type="integer" min="0" max="100" value="90" label="Report Nx, Lx, etc metrics for specific value of 'x'" help="Value of 'x' for Nx, Lx, NGx, NGAx, etc metrics reported in addition to N50, L50, NG50, NGA50, etc" />
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	457 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	458 <param name="output_files" type="select" display="checkboxes" optional="true" multiple="true" label="Output files">
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	459 <option value="html" selected="true">HTML reports</option>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	460 <option value="pdf">PDF reports</option>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	461 <option value="tabular">Tabular reports</option>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	462 <option value="log">Log file</option>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	463 <option value="summary">Key metric summary (metagenome mode)</option>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	464 <option value="krona">Krona charts (metagenome mode without reference genomes)</option>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	465 </param>
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	466 </inputs>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	467 <outputs>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	468 <data name="report_tabular" format="tabular" label="${tool.name} on ${on_string}: tabular report" from_work_dir="outputdir/report.tsv">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	469 <filter>assembly['type'] == 'genome' and 'tabular' in output_files</filter>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	470 </data>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	471 <data name="report_tabular_meta" format="tabular" label="${tool.name} on ${on_string}: tabular report for combined reference genome" from_work_dir="outputdir/combined_reference/report.tsv">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	472 <filter>assembly['type'] == 'metagenome' and 'tabular' in output_files</filter>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	473 </data>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	474 <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html">
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	475 <filter>assembly['type'] == 'genome' and 'html' in output_files</filter>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	476 </data>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	477 <data name="report_html_meta" format="html" label="${tool.name} on ${on_string}: HTML report for combined reference genome" from_work_dir="outputdir/combined_reference/report.html">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	478 <filter>assembly['type'] == 'metagenome' and 'html' in output_files</filter>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	479 </data>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	480 <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF report" from_work_dir="outputdir/report.pdf">
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	481 <filter>assembly['type'] == 'genome' and 'pdf' in output_files</filter>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	482 </data>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	483 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log">
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	484 <filter>assembly['type'] == 'genome' and 'log' in output_files</filter>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	485 </data>
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	486 <data name="log_meta" format="txt" label="${tool.name} on ${on_string}: Log Meta" from_work_dir="outputdir/metaquast.log">
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	487 <filter>assembly['type'] == 'metagenome' and 'log' in output_files</filter>
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	488 </data>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	489 <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies report" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	490 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	491 <filter>'tabular' in output_files</filter>
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	492 </data>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	493 <data name="unalign" format="tabular" label="${tool.name} on ${on_string}: Unaligned contigs report" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	494 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	495 <filter>'tabular' in output_files</filter>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	496 </data>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	497 <data name="kmers" format="tabular" label="${tool.name} on ${on_string}: K-mer-based metrics report" from_work_dir="outputdir/k_mer_stats/kmers_report.txt">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	498 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['k_mer']['k_mer_stats'] != ''</filter>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	499 <filter>'tabular' in output_files</filter>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	500 </data>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	501 <data name="circos_output" format="png" from_work_dir="outputdir/circos/circos.png" label="${tool.name} on ${on_string}: Circos plot">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	502 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['circos']</filter>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	503 </data>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	504 <collection name="metrics_tabular" type="list" label="${tool.name} on ${on_string}: Tabular reports for key metrics" >
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	505 <discover_datasets pattern="(?P<designation>.+).tsv" directory="outputdir/summary/TSV/" format="tabular"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	506 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	507 </collection>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	508 <collection name="metrics_pdf" type="list" label="${tool.name} on ${on_string}: PDF reports for key metrics" >
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	509 <discover_datasets pattern="(?P<designation>.+).pdf" directory="outputdir/summary/PDF/" format="pdf"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	510 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	511 </collection>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	512 <data name="krona" format="html" label="${tool.name} on ${on_string}: Krona chart" from_work_dir="outputdir/krona_charts/*.html">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	513 <filter>assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'none' and 'krona' in output_files</filter>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	514 </data>
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	515 </outputs>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	516 <tests>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	517 <!-- Test 01: reference, genes annotations and operon coordinates -->
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	518 <test expect_num_outputs="2">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	519 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	520 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	521 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	522 <param name="custom" value="true"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	523 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	524 <param name="input" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	525 <param name="labels" value="contig1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	526 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	527 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	528 <param name="input" value="contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	529 <param name="labels" value="contig2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	530 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	531 </conditional>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	532 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	533 <conditional name="assembly">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	534 <param name="type" value="genome"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	535 <conditional name="ref">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	536 <param name="use_ref" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	537 <param name="r" value="reference.fna"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	538 <param name="features" value="genes.gff"/>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	539 <param name="operons" value="operons.bed"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	540 <conditional name="k_mer">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	541 <param name="k_mer_stats" value="--k-mer-stats"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	542 <param name="k_mer_size" value="101" />
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	543 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	544 <param name="circos" value="true"/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	545 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	546 <param name="orga_type" value=""/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	547 </conditional>
f30d03867854 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_contig" value="500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	549 <param name="split_scaffolds" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	550 <section name="genes">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	551 <conditional name="gene_finding">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	552 <param name="tool" value="--gene_finding"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	553 <param name="gene_thresholds" value="0,300,1500,3000"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	554 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	555 <param name="rna_finding" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	556 <param name="conserved_genes_finding" value="true"/>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	557 <param name="min_identity" value="95.0"/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	558 </section>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	559 <section name="alignments">
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	560 <param name="use_all_alignments" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	561 <param name="min_alignment" value="65"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	562 <param name="ambiguity_usage" value="one"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	563 <param name="ambiguity_score" value="0.99"/>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	564 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	565 <section name="advanced">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	566 <param name="contig_thresholds" value="0,1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	567 <param name="strict_NA" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	568 <param name="extensive_mis_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	569 <param name="scaffold_gap_max_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	570 <param name="unaligned_part_size" value="500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	571 <param name="skip_unaligned_mis_contigs" value="true"/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	572 <param name="fragmented_max_indent" value="50"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	573 </section>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	574 <param name="output_files" value="html"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	575 <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/>
12 875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 11 diff changeset	576 <output name="circos_output" file="test1_circos.png" ftype="png" compare="sim_size"/>
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	577 </test>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	578 <!-- Test 02: all outputs -->
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	579 <test expect_num_outputs="8">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	580 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	581 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	582 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	583 <param name="custom" value="true"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	584 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	585 <param name="input" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	586 <param name="labels" value="contig1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	587 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	588 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	589 <param name="input" value="contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	590 <param name="labels" value="contig2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	591 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	592 </conditional>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	593 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	594 <conditional name="assembly">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	595 <param name="type" value="genome"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	596 <conditional name="ref">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	597 <param name="use_ref" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	598 <param name="r" value="reference.fna"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	599 <param name="features" value="genes.gff"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	600 <param name="operons" value="operons.bed"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	601 <conditional name="k_mer">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	602 <param name="k_mer_stats" value="--k-mer-stats"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	603 <param name="k_mer_size" value="101" />
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	604 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	605 <param name="circos" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	606 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	607 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	608 <param name="output_files" value="html,pdf,tabular,log"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	609 <output name="report_html" file="test2_report.html" ftype="html" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	610 <output name="report_pdf" file="test2_report.pdf" ftype="pdf" compare="sim_size"/>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	611 <output name="report_tabular" file="test2_report.tab" ftype="tabular"/>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	612 <output name="log" file="test2.log" ftype="txt" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	613 <output name="mis_ass" file="test2_missasemblies.tab" ftype="tabular"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	614 <output name="unalign" file="test2_unaligned.tab" ftype="tabular"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	615 <output name="kmers" file="test2_kmers.tab" ftype="tabular"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	616 <output name="circos_output" file="test2_circos.png" ftype="png" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	617 </test>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	618 <!-- Test 03: without reference -->
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	619 <test expect_num_outputs="3">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	620 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	621 <param name="mode" value="individual"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	622 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	623 <param name="custom" value="false"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	624 <param name="inputs" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	625 </conditional>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	626 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	627 <conditional name="assembly">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	628 <param name="type" value="genome"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	629 <conditional name="ref">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	630 <param name="use_ref" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	631 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	632 <param name="orga_type" value="--eukaryote"/>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	633 <param name="min_identity" value="95.0"/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	634 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	635 <param name="min_contig" value="500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	636 <param name="split_scaffolds" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	637 <param name="large" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	638 <section name="genes">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	639 <conditional name="gene_finding">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	640 <param name="tool" value="none"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	641 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	642 <param name="rna_finding" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	643 <param name="conserved_genes_finding" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	644 </section>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	645 <section name="alignments">
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	646 <param name="use_all_alignments" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	647 <param name="min_alignment" value="65"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	648 <param name="ambiguity_usage" value="one"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	649 <param name="ambiguity_score" value="0.99"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	650 <param name="fragmented" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	651 </section>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	652 <section name="advanced">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	653 <param name="contig_thresholds" value="0,1000, 500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	654 <param name="strict_NA" value="false"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	655 <param name="extensive_mis_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	656 <param name="scaffold_gap_max_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	657 <param name="unaligned_part_size" value="500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	658 <param name="skip_unaligned_mis_contigs" value="-"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	659 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	660 <param name="output_files" value="html,pdf,log" />
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	661 <output name="log" file="test3.log" ftype="txt" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	662 <output name="report_html" file="test3_report.html" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	663 <output name="report_pdf" file="test3_report.pdf" compare="sim_size"/>
3 6fcbee531de6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67 iuc parents: 2 diff changeset	664 </test>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	665 <!-- Test 04: metagenomics -->
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	666 <test expect_num_outputs="3">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	667 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	668 <param name="mode" value="individual"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	669 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	670 <param name="custom" value="false"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	671 <param name="inputs" value="contigs3.fasta"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	672 </conditional>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	673 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	674 <conditional name="assembly">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	675 <param name="type" value="metagenome"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	676 <conditional name="ref">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	677 <param name="origin" value="silva"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	678 <param name="max_ref_num" value="50"/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	679 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	680 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	681 <param name="min_contig" value="500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	682 <param name="split_scaffolds" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	683 <param name="large" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	684 <section name="genes">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	685 <conditional name="gene_finding">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	686 <param name="tool" value="--mgm"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	687 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	688 <param name="rna_finding" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	689 <param name="conserved_genes_finding" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	690 </section>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	691 <section name="alignments">
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	692 <param name="use_all_alignments" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	693 <param name="min_alignment" value="65"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	694 <param name="min_identity" value="95.0"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	695 <param name="ambiguity_usage" value="one"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	696 <param name="ambiguity_score" value="0.99"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	697 <param name="fragmented" value="false"/>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	698 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	699 <section name="advanced">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	700 <param name="contig_thresholds" value="0,1000, 500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	701 <param name="strict_NA" value="false"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	702 <param name="extensive_mis_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	703 <param name="scaffold_gap_max_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	704 <param name="unaligned_part_size" value="500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	705 <param name="skip_unaligned_mis_contigs" value="-"/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	706 </section>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	707 <param name="output_files" value="log,html,tabular"/>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	708 <output name="log_meta" ftype="txt">
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	709 <assert_contents>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	710 <has_text text="Reference genomes are not found" />
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	711 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	712 </output>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	713 <output name="report_tabular_meta" ftype="tabular">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	714 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	715 <has_text text="# contigs (>= 0 bp)"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	716 <has_text text="contigs3_fasta"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	717 <has_text text="# N's per 100 kbp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	718 <has_n_lines n="17"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	719 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	720 </output>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	721 <output name="report_html_meta" ftype="html">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	722 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	723 <has_text text="Quality Assessment Tool for Genome Assemblies" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	724 <has_text text="contigs3_fasta" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	725 <has_text text="Statistics without reference" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	726 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	727 </output>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	728 </test>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	729 <!-- Test 05: FASTQ read files -->
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	730 <test expect_num_outputs="3">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	731 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	732 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	733 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	734 <param name="custom" value="true"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	735 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	736 <param name="input" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	737 <param name="labels" value="contig1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	738 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	739 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	740 <param name="input" value="contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	741 <param name="labels" value="contig2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	742 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	743 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	744 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	745 <param name="reads_option" value="pacbio"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	746 <param name="input_1" value="pacbio_01.fastq,pacbio_02.fastq,pacbio_03.fastq,pacbio_04.fastq"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	747 </conditional>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	748 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	749 <conditional name="assembly">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	750 <param name="type" value="genome"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	751 <conditional name="ref">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	752 <param name="use_ref" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	753 <param name="r" value="reference.fna"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	754 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	755 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	756 <section name="alignments">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	757 <param name="upper_bound_assembly" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	758 <param name="upper_bound_min_con" value="1"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	759 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	760 <param name="output_files" value="tabular"/>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	761 <output name="report_tabular" file="test5.tab" ftype="tabular"/>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	762 <output name="mis_ass" ftype="tabular">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	763 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	764 <has_text text="All statistics are based on contigs of size >= 500 bp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	765 <has_text text="# scaffold misassemblies"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	766 <has_text text="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	767 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	768 </output>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	769 <output name="unalign" ftype="tabular">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	770 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	771 <has_text text="Fully unaligned length"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	772 <has_text text="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	773 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	774 </output>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	775 </test>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	776 <!-- Test 06: FASTQ.gz read files -->
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	777 <test expect_num_outputs="1">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	778 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	779 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	780 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	781 <param name="custom" value="true"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	782 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	783 <param name="input" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	784 <param name="labels" value="contig1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	785 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	786 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	787 <param name="input" value="contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	788 <param name="labels" value="contig2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	789 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	790 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	791 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	792 <param name="reads_option" value="single"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	793 <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	794 </conditional>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	795 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	796 <param name="output_files" value="tabular"/>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	797 <output name="report_tabular" file="test6.tab" ftype="tabular"/>
6 f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b iuc parents: 5 diff changeset	798 </test>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	799 <!-- Test 07: FASTA.gz read files -->
12 875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 11 diff changeset	800 <test expect_num_outputs="1">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	801 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	802 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	803 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	804 <param name="custom" value="true"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	805 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	806 <param name="input" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	807 <param name="labels" value="contig1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	808 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	809 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	810 <param name="input" value="contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	811 <param name="labels" value="contig2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	812 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	813 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	814 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	815 <param name="reads_option" value="single"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	816 <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	817 </conditional>
12 875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 11 diff changeset	818 </conditional>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 11 diff changeset	819 <param name="output_files" value="tabular"/>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	820 <output name="report_tabular" file="test7.tab" ftype="tabular"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	821 </test>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	822 <!-- Test 08: metagenomics all tab outputs-->
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	823 <test expect_num_outputs="3">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	824 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	825 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	826 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	827 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	828 <param name="input" value="meta_contigs_1.fasta"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	829 <param name="labels" value="meta_contigs_1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	830 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	831 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	832 <param name="input" value="meta_contigs_2.fasta"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	833 <param name="labels" value="meta_contigs_2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	834 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	835 </conditional>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	836 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	837 <conditional name="assembly">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	838 <param name="type" value="metagenome"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	839 <conditional name="ref">
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	840 <param name="origin" value="history"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	841 <param name="r" value="meta_ref_1.fasta,meta_ref_2.fasta,meta_ref_3.fasta"/>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	842 </conditional>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	843 <param name="min_identity" value="95.0"/>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	844 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	845 <param name="min_contig" value="500"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	846 <param name="split_scaffolds" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	847 <param name="large" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	848 <section name="genes">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	849 <conditional name="gene_finding">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	850 <param name="tool" value="none"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	851 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	852 <param name="rna_finding" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	853 <param name="conserved_genes_finding" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	854 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	855 <section name="alignments">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	856 <param name="use_all_alignments" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	857 <param name="min_alignment" value="65"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	858 <param name="ambiguity_usage" value="one"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	859 <param name="ambiguity_score" value="0.99"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	860 <param name="fragmented" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	861 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	862 <section name="advanced">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	863 <param name="contig_thresholds" value="0,1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	864 <param name="strict_NA" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	865 <param name="extensive_mis_size" value="1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	866 <param name="scaffold_gap_max_size" value="1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	867 <param name="unaligned_part_size" value="500"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	868 <param name="skip_unaligned_mis_contigs" value="-"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	869 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	870 <param name="output_files" value="tabular,summary"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	871 <output name="report_tabular_meta" ftype="tabular">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	872 <assert_contents>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	873 <has_text text="# contigs (>= 0 bp)"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	874 <has_text text="meta_ref_3_fasta"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	875 <has_text text="# N's per 100 kbp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	876 <has_n_lines n="34"/>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	877 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	878 </output>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	879 <output_collection name="metrics_tabular" type="list" count="15"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	880 <output_collection name="metrics_pdf" type="list" count="16"/>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	881 </test>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	882 <!-- Test 09: metagenomics log, html and krona outputs-->
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	883 <test expect_num_outputs="2">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	884 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	885 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	886 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	887 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	888 <param name="input" value="meta_contigs_1.fasta"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	889 <param name="labels" value="meta_contigs_1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	890 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	891 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	892 <param name="input" value="meta_contigs_2.fasta"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	893 <param name="labels" value="meta_contigs_2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	894 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	895 </conditional>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	896 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	897 <conditional name="assembly">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	898 <param name="type" value="metagenome"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	899 <conditional name="ref">
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	900 <param name="origin" value="list"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	901 <param name="references_list" value="Lactobacillus_delbrueckii_bulgaricus,Lactobacillus_reuteri"/>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	902 </conditional>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	903 <param name="min_identity" value="95.0"/>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	904 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	905 <param name="min_contig" value="500"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	906 <param name="split_scaffolds" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	907 <param name="large" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	908 <section name="genes">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	909 <conditional name="gene_finding">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	910 <param name="tool" value="none"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	911 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	912 <param name="rna_finding" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	913 <param name="conserved_genes_finding" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	914 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	915 <section name="alignments">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	916 <param name="use_all_alignments" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	917 <param name="min_alignment" value="65"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	918 <param name="ambiguity_usage" value="all"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	919 <param name="ambiguity_score" value="0.99"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	920 <param name="fragmented" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	921 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	922 <section name="advanced">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	923 <param name="contig_thresholds" value="0,1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	924 <param name="strict_NA" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	925 <param name="extensive_mis_size" value="1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	926 <param name="scaffold_gap_max_size" value="1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	927 <param name="unaligned_part_size" value="500"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	928 <param name="skip_unaligned_mis_contigs" value="-"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	929 </section>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	930 <param name="output_files" value="html,log"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	931 <output name="report_html_meta" ftype="html">
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	932 <assert_contents>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	933 <has_text text="meta_contigs_2_fasta" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	934 <has_text text="combined_reference" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	935 <has_text text="Lactobacillus" />
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	936 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	937 </output>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	938 <output name="log_meta" ftype="txt">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	939 <assert_contents>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	940 <has_text text="List of references was provided, starting to download reference genomes from NCBI" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	941 <has_text text="Lactobacillus_delbrueckii_bulgaricus" />
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	942 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	943 </output>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	944 </test>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	945 <!-- Test 10: Test new options -->
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	946 <test expect_num_outputs="1">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	947 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	948 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	949 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	950 <param name="custom" value="true"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	951 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	952 <param name="input" value="contigs1.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	953 <param name="labels" value="contig1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	954 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	955 <repeat name="inputs">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	956 <param name="input" value="contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	957 <param name="labels" value="contig2"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	958 </repeat>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	959 </conditional>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	960 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	961 <section name="alignments">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	962 <param name="local_mis_size" value="210"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	963 </section>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	964 <conditional name="assembly">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	965 <param name="type" value="genome"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	966 <conditional name="ref">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	967 <param name="use_ref" value="false"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	968 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	969 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	970 <section name="advanced">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	971 <param name="report_all_metrics" value="true"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	972 <param name="x_for_Nx" value="80"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	973 </section>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	974 <param name="output_files" value="tabular"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	975 <output name="report_tabular" file="test10_tabular_report.tab" ftype="tabular"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	976 </test>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	977 <!-- Test 11: Test paired fastq.gz inputs -->
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	978 <test expect_num_outputs="1">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	979 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	980 <param name="mode" value="individual"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	981 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	982 <param name="custom" value="true"/>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	983 <param name="input" value="contigs1.fna"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	984 <param name="labels" value="contig1"/>
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	985 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	986 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	987 <param name="reads_option" value="paired"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	988 <param name="input_1" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	989 <param name="input_2" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	990 </conditional>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	991 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	992 <conditional name="assembly">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	993 <param name="type" value="genome"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	994 <conditional name="ref">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	995 <param name="use_ref" value="false"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	996 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	997 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	998 <param name="output_files" value="tabular"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	999 <output name="report_tabular" ftype="tabular">
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	1000 <assert_contents>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1001 <has_text text="# contigs (>= 0 bp)"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1002 <has_text text="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1003 <has_text text="# N's per 100 kbp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1004 <has_n_lines n="22"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1005 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1006 </output>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1007 </test>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1008 <!-- Test 12: Test paired-collection fastq.gz inputs -->
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1009 <test expect_num_outputs="1">
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1010 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1011 <param name="mode" value="individual"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1012 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1013 <param name="custom" value="true"/>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1014 <param name="input" value="contigs1.fna"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1015 <param name="labels" value="contig1"/>
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1016 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1017 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1018 <param name="reads_option" value="paired_collection"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1019 <param name="input_1">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1020 <collection type="paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1021 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1022 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1023 </collection>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1024 </param>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1025 </conditional>
14 3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1026 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1027 <conditional name="assembly">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1028 <param name="type" value="genome"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1029 <conditional name="ref">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1030 <param name="use_ref" value="false"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1031 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1032 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1033 <param name="output_files" value="tabular"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1034 <output name="report_tabular" ftype="tabular">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1035 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1036 <has_text text="# contigs (>= 0 bp)"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1037 <has_text text="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1038 <has_text text="# N's per 100 kbp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 iuc parents: 13 diff changeset	1039 <has_n_lines n="15"/>
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	1040 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	1041 </output>
12 875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86" iuc parents: 11 diff changeset	1042 </test>
15 72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1043 <!-- Test 13: Test co-assembly with paired-collection fastq.gz inputs -->
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1044 <test expect_num_outputs="1">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1045 <conditional name="mode">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1046 <param name="mode" value="co"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1047 <conditional name="in">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1048 <param name="custom" value="false"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1049 <param name="inputs" value="contigs1.fna,contigs2.fna"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1050 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1051 <conditional name="reads">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1052 <param name="reads_option" value="paired_collection"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1053 <param name="input_1">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1054 <collection type="list:paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1055 <element name="s1">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1056 <collection type="paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1057 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1058 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1059 </collection>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1060 </element>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1061 <element name="s2">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1062 <collection type="paired">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1063 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1064 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1065 </collection>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1066 </element>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1067 </collection>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1068 </param>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1069 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1070 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1071 <conditional name="assembly">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1072 <param name="type" value="genome"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1073 <conditional name="ref">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1074 <param name="use_ref" value="false"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1075 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1076 </conditional>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1077 <param name="output_files" value="tabular"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1078 <output name="report_tabular" ftype="tabular">
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1079 <assert_contents>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1080 <has_text text="# contigs (>= 0 bp)"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1081 <has_text text="contigs1"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1082 <has_text text="# N's per 100 kbp"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1083 <has_n_lines n="22"/>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1084 </assert_contents>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1085 </output>
72472698a2df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 iuc parents: 14 diff changeset	1086 </test>
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1087 </tests>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1088 <help>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1089 <![CDATA[
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1090 What it does
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1091
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1092 QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1093
8 ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1094 If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page <http://quast.sourceforge.net/docs/manual.html>`_.
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1095
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1096 Using Quast without reference
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1097
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1098 Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments car, pit, and cef (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs:
13 675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb" iuc parents: 12 diff changeset	1099
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1100 * Quast report in HTML format
8 ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1101 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1102 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1103 * Quast log (a file technical information about Quast tool execution)
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1104
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1105 The tab delimited Quast report will contain the following information::
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1106
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1107 Assembly pit_fna cef_fna car_fna
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1108 # contigs (>= 0 bp) 100 91 94
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1109 # contigs (>= 1000 bp) 62 58 61
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1110 Total length (>= 0 bp) 6480635 6481216 6480271
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1111 Total length (>= 1000 bp) 6466917 6468946 6467103
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1112 # contigs 71 66 70
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1113 Largest contig 848753 848766 662053
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1114 Total length 6473173 6474698 6473810
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1115 GC (%) 66.33 66.33 66.33
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1116 N50 270269 289027 254671
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1117 N75 136321 136321 146521
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1118 L50 7 7 8
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1119 L75 15 15 16
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1120 # N's per 100 kbp 0.00 0.00 0.00
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1121
8 ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1122 where values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1123
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1124 Quast report in HTML format contains graphs in addition to the above metrics, while Contig viewer draws contigs ordered from longest to shortest. This ordering is suitable for comparing only largest contigs or number of contigs longer than a specific threshold. The viewer shows N50 and N75 with color and textual indication. If the reference genome is available or at least approximate genome length is known (see `--est-ref-size`), NG50 and NG75 are also shown. You can also tone down contigs shorter than a specified threshold using Icarus control panel:
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1125
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1126 .. image:: $PATH_TO_IMAGES/contig_view_noR.png
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1127 :width: 558
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1128 :height: 412
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1129
8 ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1130 Also see `Plot description <http://quast.sourceforge.net/docs/manual.html#sec2>`_ section of the manual.
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1131
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1132 Using Quast with reference
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1133
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1134 Car, pit, and cef are in fact assemblies of Pseudomonas aeruginosa UCBPP-PA14, so we can use its genome as a reference (by supplying a Fasta file containing P. aeruginosa pa14 genome to Reference genome input box). The following outputs will be produced (note the alignment viewer):
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1135
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1136 * Quast report in HTML format
8 ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1137 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1138 * `Alignment viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1139 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1140 * Summary of `misassemblies <http://quast.sourceforge.net/docs/manual.html#sec3.1.2>`_
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1141 * Summary of `unaligned contigs <http://quast.sourceforge.net/docs/manual.html#sec3.1.3>`_
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1142 * Quast log (a file technical information about Quast tool execution)
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1143
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1144 With the reference Quast produces a much more comprehensive set of results::
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1145
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1146 Assembly pit_fna cef_fna car_fna
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1147 # contigs (>= 0 bp) 100 91 94
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1148 # contigs (>= 1000 bp) 62 58 61
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1149 Total length (>= 0 bp) 6480635 6481216 6480271
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1150 Total length (>= 1000 bp) 6466917 6468946 6467103
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1151 # contigs 71 66 70
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1152 Largest contig 848753 848766 662053
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1153 Total length 6473173 6474698 6473810
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1154 Reference length 6537648 6537648 6537648
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1155 GC (%) 66.33 66.33 66.33
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1156 Reference GC (%) 66.29 66.29 66.29
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1157 N50 270269 289027 254671
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1158 NG50 270269 289027 254671
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1159 N75 136321 136321 146521
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1160 NG75 136321 136321 136321
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1161 L50 7 7 8
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1162 LG50 7 7 8
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1163 L75 15 15 16
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1164 LG75 15 15 17
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1165 # misassemblies 0 0 0
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1166 # misassembled contigs 0 0 0
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1167 Misassembled contigs length 0 0 0
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1168 # local misassemblies 1 1 2
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1169 # unaligned mis. contigs 0 0 0
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1170 # unaligned contigs 0 + 0 0 + 0 0 + 0
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1171 part part part
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1172 Unaligned length 0 0 0
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1173 Genome fraction (%) 99.015 99.038 99.025
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1174 Duplication ratio 1.000 1.000 1.000
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1175 # N's per 100 kbp 0.00 0.00 0.00
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1176 # mismatches per 100 kbp 3.82 3.63 3.49
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1177 # indels per 100 kbp 1.19 1.13 1.13
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1178 Largest alignment 848753 848766 662053
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1179 Total aligned length 6473163 6474660 6473792
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1180 NA50 270269 289027 254671
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1181 NGA50 270269 289027 254671
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1182 NA75 136321 136321 146521
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1183 NGA75 136321 136321 136321
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1184 LA50 7 7 8
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1185 LGA50 7 7 8
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1186 LA75 15 15 16
8 ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1187 LGA75 15 15 17
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1188
8 ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1189 where, again, values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_. You can see that this report includes a variety of data that can only be computer against a reference assembly.
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1190
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	1191 Using reference also produces an Alignment viewer:
4 0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1192
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1193 .. image:: $PATH_TO_IMAGES/Align_view.png
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1194 :width: 515
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1195 :height: 395
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87 iuc parents: 3 diff changeset	1196
8 ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78" iuc parents: 7 diff changeset	1197 Alignment viewer highlights regions of interest as, in this case, missassemblies that can potentially point to genome rearrangements (see more `here <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_).
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1198
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1199 ]]>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1200 </help>
9 45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414" iuc parents: 8 diff changeset	1201 <expand macro="citations"/>
0 736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 iuc parents: diff changeset	1202 </tool>

Mercurial > repos > iuc > quast

annotate quast.xml @ 15:72472698a2df draft default tip