Mercurial > repos > iuc > quast

annotate quast.xml @ 8:ebb0dcdb621a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
author iuc
date Mon, 03 Feb 2020 17:37:36 -0500
parents 59db8ea8c845
children 45924fa8d8c5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
1 <tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy1" profile="18.01">
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>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
4 <token name="@TOOL_VERSION@">5.0.2</token>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
5 <xml name="gene_thresholds">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
6 <param name="gene_thresholds" argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
7 </xml>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
8 </macros>
0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
9 <requirements>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
10 <requirement type="package" version="@TOOL_VERSION@">quast</requirement>
0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
11 </requirements>
5
81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents: 4
diff changeset
12 <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
13 <![CDATA[
5
81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents: 4
diff changeset
14 #import re
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
15
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
16 #if str($in.custom) == 'false'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
17 #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $in.inputs ])
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
18 #else
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
19 #set $labels = []
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
20 #for $x in $in.inputs
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
21 #if str($x.labels) != ''
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
22 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels)))
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
23 #else
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
24 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.input.element_identifier)))
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
25 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
26 #end for
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
27 #set $labels = ','.join($labels)
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
28 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
29
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
30 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
31 #set $temp_ref_list_fp = 'temp_ref_list_fp'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
32 #set $temp_ref_list_f = open($temp_ref_list_fp, 'w')
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
33 #silent $temp_ref_list_f.write('\n'.join([x.strip() for x in $assembly.ref.references_list.split(',')]))
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
34 #silent $temp_ref_list_f.close()
5
81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents: 4
diff changeset
35 #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
36
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
37 #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
38 quast
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
39 #else
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
40 metaquast
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
41 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
42 -o outputdir
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
43
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
44 #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
45 #if $assembly.ref.use_ref == 'true'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
46 -r '$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
47 #if $assembly.ref.features
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
48 --features '$assembly.ref.features'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
49 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
50 #if $assembly.ref.operons
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
51 --operons '$assembly.ref.operons'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
52 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
53 #else if $assembly.ref.est_ref_size
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
54 --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
55 #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
56 $assembly.orga_type
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
57 #else
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
58 #if $assembly.ref.origin == 'history'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
59 -r '$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
60 #else if $assembly.ref.origin == 'list'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
61 --references-list '$temp_ref_list_fp'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
62 #else if $assembly.ref.origin == 'silva'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
63 --test-no-ref
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
64 --max-ref-num '$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
65 #end if
81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents: 4
diff changeset
66 #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
67 --min-contig $min_contig
7
59db8ea8c845 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 82c339e6bc07c98765bcfb56f34520ac38648267
iuc
parents: 6
diff changeset
68 --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
69 $split_scaffolds
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
70 --labels $labels
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
71 $large
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
72 $k_mer.k_mer_stats
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
73 #if str($k_mer.k_mer_stats) != ''
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
74 --k-mer-size $k_mer.k_mer_size
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 $circos
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
77 #if str($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
78 $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
79 #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
80 #set $gene_threshold = ','.join([x.strip() for x in str($genes.gene_finding.gene_thresholds).split(',')])
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
81 --gene-thresholds '$gene_threshold'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
82 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
83 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
84 $genes.rna_finding
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
85 $genes.conserved_genes_finding
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
86 $al.use_all_alignments
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
87 --min-alignment $al.min_alignment
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
88 --min-identity $al.min_identity
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
89 --ambiguity-usage '$al.ambiguity_usage'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
90 $al.fragmented
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
91 #set $contig_thresholds = ','.join([x.strip() for x in str($contig_thresholds).split(',')])
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
92 --contig-thresholds '$contig_thresholds'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
93 $strict_NA
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
94 --extensive-mis-size $extensive_mis_size
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
95 --scaffold-gap-max-size $scaffold_gap_max_size
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
96 --unaligned-part-size $unaligned_part_size
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
97 $skip_unaligned_mis_contigs
3
6fcbee531de6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
iuc
parents: 2
diff changeset
98
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
99 #if str($in.custom) == 'false'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
100 #for $k in $in.inputs
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
101 '$k'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
102 #end for
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
103 #else
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
104 #for $k in $in.inputs
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
105 '$k.input'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
106 #end for
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
107 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
108
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
109 && mkdir -p '$report_html.files_path'
5
81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents: 4
diff changeset
110 && cp outputdir/*.html '$report_html.files_path'
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
111 #if ($assembly.type == 'genome' and $assembly.ref.use_ref) or ($assembly.type == 'metagenome' and $assembly.ref.origin != 'none')
5
81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents: 4
diff changeset
112 && cp -R outputdir/icarus_viewers '$report_html.files_path'
81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents: 4
diff changeset
113 #end if
0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
114 ]]>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
115 </command>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
116 <inputs>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
117 <conditional name="in">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
118 <param name="custom" type="select" label="Use customized names for the input files?" help="They will be used in reports, plots and logs">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
119 <option value="true">Yes, specify custom names for</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
120 <option value="false" selected="true">No, use dataset names</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
121 </param>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
122 <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
123 <repeat name="inputs" title="Contigs/scaffolds" min="1">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
124 <param name="input" type="data" format="fasta" label="Contigs/scaffolds file"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
125 <param argument="--labels" type="text" value="" label="Name"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
126 </repeat>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
127 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
128 <when value="false">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
129 <param name="inputs" type="data" format="fasta" multiple="true" label="Contigs/scaffolds file"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
130 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
131 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
132 <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
133 <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
134 <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
135 <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
136 </param>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
137 <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
138 <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
139 <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
140 <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
141 <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
142 </param>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
143 <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
144 <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
145 <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
146 <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"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
147 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
148 <when value="false">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
149 <param name="est_ref_size" argument="--est-ref-size" type="integer" optional="true" label="Estimated reference genome size (in bp) for computing NGx statistics" help=""/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
150 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
151 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
152 <param name="orga_type" type="select" label="Type of organism">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
153 <option value="">Prokaryotes: use of GeneMarkS for gene finding</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
154 <option value="--eukaryote">Eukaryote (--eukaryote): use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
155 <option value="--fungus">Fungus (--fungus): use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
156 </param>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
157 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
158 <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
159 <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
160 <param name="origin" type="select" label="Reference genome" help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference.">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
161 <option value="history">From history</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
162 <option value="list">From list</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
163 <option value="silva">From SILVA database</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
164 <option value="none" selected="true">None</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
165 </param>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
166 <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
167 <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
168 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
169 <when value="list">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
170 <param name="references_list" argument="references-list" type="text" value="" label="Comma-separated list of reference genomes" help="MetaQUAST will search for these references in the NCBI database and will download the found ones"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
171 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
172 <when value="silva">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
173 <param name="max_ref_num" argument="-max-ref-num" type="integer" value="50" label="Maximum number of reference genomes (per each assembly) to download after searching in the SILVA databa" />
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
174 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
175 <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
176 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
177 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
178 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
179 <param name="min_contig" 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"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
180 <param name="split_scaffolds" 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."/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
181 <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
182 <conditional name="k_mer">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
183 <param name="k_mer_stats" 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">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
184 <option value="--k-mer-stats">Yes</option>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
185 <option value="" 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
186 </param>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
187 <when value="--k-mer-stats">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
188 <param name="k_mer_size" argument="--k-mer-size" type="integer" value="101" label="Size of k" />
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
189 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
190 <when value=""/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
191 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
192 <param argument="--circos" type="boolean" truevalue="--circos" falsevalue="" checked="false" label="Draw Circos plot?" help=""/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
193 <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
194 <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
195 <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
196 <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
197 <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
198 <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
199 <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
200 </param>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
201 <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
202 <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
203 <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
204 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
205 <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
206 <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
207 <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
208 </when>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
209 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
210 <param name="rna_finding" 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. "/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
211 <param name="conserved_genes_finding" 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. "/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
212 </section>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
213 <section name="al" title="Alignments">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
214 <param name="use_all_alignments" 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)"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
215 <param name="min_alignment" 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."/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
216 <param name="min_identity" argument="--min-identity" type="float" value="95.0" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. ote that all alignments with IDY% less than 80.0% will be filtered regardless of this threshold. "/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
217 <param name="ambiguity_usage" argument="--ambiguity-usage" type="select" label="How processing equally good alignments of a contig (probably repeats)?" help="">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
218 <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
219 <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
220 <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
221 </param>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
222 <param name="ambiguity_score" 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. "/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
223 <param argument="--fragmented" type="boolean" truevalue="--fragmented" 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)"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
224 <param name="fragmented_max_indent" argument="--fragmented-max-indent" type="integer" value="50" label="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments" help="The value should be less than extensive misassembly size"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
225 <param name="upper_bound_assembly" argument="--upper-bound-assembly" type="boolean" truevalue="--upper-bound-assembly" falsevalue="" checked="false" label="Simulate upper bound assembly based on the reference genome and a given set reads?" help="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. See Mikheenko et al., 2018 for more details. "/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
226 <param name="upper_bound_min_con" argument="--upper-bound-min-con" type="integer" value="2" 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)."/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
227 </section>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
228 <param name="contig_thresholds" 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"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
229 <param name="strict_NA" 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)."/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
230 <param name="extensive_mis_size" 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."/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
231 <param name="scaffold_gap_max_size" 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"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
232 <param name="unaligned_part_size" argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
233 <param name="skip_unaligned_mis_contigs" 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)."/>
0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
234 </inputs>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
235 <outputs>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
236 <data name="quast_tabular" format="tabular" label="${tool.name} on ${on_string}: tabular report" from_work_dir="outputdir/report.tsv"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
237 <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
238 <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF report" from_work_dir="outputdir/report.pdf"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
239 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
240 <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
241 <filter>(assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true') or (assembly['type'] == 'metagenome' and assembly['ref']['origin'] != 'none')</filter>
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
242 </data>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
243 <data name="unalign" format="tabular" label="${tool.name} on ${on_string}: Unaligned contigs" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
244 <filter>(assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true') or (assembly['type'] == 'metagenome' and assembly['ref']['origin'] != 'none')</filter>
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
245 </data>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
246 <data name="kmers" format="tabular" label="${tool.name} on ${on_string}: K-mer-based metrics" from_work_dir="outputdir/k_mer_stats/kmers_report.txt">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
247 <filter>k_mer['k_mer_stats'] != ''</filter>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
248 </data>
0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
249 </outputs>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
250 <tests>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
251 <test>
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
252 <!-- Test with reference and genes annotations -->
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
253 <conditional name="in">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
254 <param name="custom" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
255 <repeat name="inputs">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
256 <param name="input" value="contigs1.fna"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
257 <param name="labels" value="contig1"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
258 </repeat>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
259 <repeat name="inputs">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
260 <param name="input" value="contigs2.fna"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
261 <param name="labels" value=""/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
262 </repeat>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
263 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
264 <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
265 <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
266 <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
267 <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
268 <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
269 <param name="features" value="genes.gff"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
270 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
271 <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
272 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
273 <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
274 <param name="split_scaffolds" value="false"/>
5
81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents: 4
diff changeset
275 <param name="large" 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
276 <conditional name="k_mer">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
277 <param name="k_mer_stats" value="--k-mer-stats"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
278 <param name="k_mer_size" value="101" />
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
279 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
280 <param name="circos" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
281 <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
282 <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
283 <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
284 <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
285 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
286 <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
287 <param name="conserved_genes_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
288 </section>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
289 <section name="al">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
290 <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
291 <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
292 <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
293 <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
294 <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
295 <param name="fragmented" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
296 <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
297 <param name="upper_bound_assembly" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
298 <param name="upper_bound_min_con" value="2"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
299 </section>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
300 <param name="contig_thresholds" value="0,1000"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
301 <param name="strict_NA" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
302 <param name="extensive_mis_size" value="1000"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
303 <param name="scaffold_gap_max_size" value="1000"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
304 <param name="unaligned_part_size" value="500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
305 <param name="skip_unaligned_mis_contigs" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
306 <output name="quast_tabular" file="test1.tabular" lines_diff="2"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
307 <output name="mis_ass" file="test1_mis_ass.tabular"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
308 <output name="unalign" file="test1_unalign.tabular"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
309 <output name="kmers" file="test1_kmers.tabular"/>
0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
310 </test>
3
6fcbee531de6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
iuc
parents: 2
diff changeset
311 <test>
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
312 <!-- Test without reference -->
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
313 <conditional name="in">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
314 <param name="custom" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
315 <param name="inputs" value="contigs1.fna,contigs2.fna"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
316 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
317 <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
318 <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
319 <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
320 <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
321 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
322 <param name="orga_type" value="--eukaryote"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
323 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
324 <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
325 <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
326 <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
327 <conditional name="k_mer">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
328 <param name="k_mer_stats" value=""/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
329 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
330 <param name="circos" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
331 <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
332 <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
333 <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
334 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
335 <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
336 <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
337 </section>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
338 <section name="al">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
339 <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
340 <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
341 <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
342 <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
343 <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
344 <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
345 <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
346 <param name="upper_bound_assembly" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
347 <param name="upper_bound_min_con" value="2"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
348 </section>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
349 <param name="contig_thresholds" value="0,1000, 500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
350 <param name="strict_NA" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
351 <param name="extensive_mis_size" value="1000"/>
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="scaffold_gap_max_size" value="1000"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
353 <param name="unaligned_part_size" value="500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
354 <param name="skip_unaligned_mis_contigs" value="-"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
355 <output name="quast_tabular" file="test2.tabular"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
356 <output name="report_html" file="test2_report.html" compare="sim_size"/>
5
81df4950d65b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents: 4
diff changeset
357 <output name="report_pdf" file="test2_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
358 </test>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
359 <test>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
360 <!-- Test with metagenomics -->
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
361 <conditional name="in">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
362 <param name="custom" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
363 <param name="inputs" value="contigs3.fasta"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
364 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
365 <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
366 <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
367 <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
368 <param name="origin" value="none"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
369 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
370 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
371 <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
372 <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
373 <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
374 <conditional name="k_mer">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
375 <param name="k_mer_stats" value=""/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
376 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
377 <param name="circos" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
378 <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
379 <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
380 <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
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="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
383 <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
384 </section>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
385 <section name="al">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
386 <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
387 <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
388 <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
389 <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
390 <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
391 <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
392 <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
393 <param name="upper_bound_assembly" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
394 <param name="upper_bound_min_con" value="2"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
395 </section>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
396 <param name="contig_thresholds" value="0,1000, 500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
397 <param name="strict_NA" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
398 <param name="extensive_mis_size" value="1000"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
399 <param name="scaffold_gap_max_size" value="1000"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
400 <param name="unaligned_part_size" value="500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
401 <param name="skip_unaligned_mis_contigs" value="-"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
402 <output name="quast_tabular" file="test3.tabular"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
403 </test>
0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
404 </tests>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
405 <help>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
406 <![CDATA[
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
407 **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
408
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
409 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
410
8
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
411 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
412
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
413 **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
414
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
415 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:
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
416
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
417 * 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
418 * `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
419 * `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
420 * 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
421
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
422 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
423
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
424 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
425 # 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
426 # 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
427 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
428 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
429 # 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
430 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
431 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
432 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
433 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
434 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
435 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
436 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
437 # 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
438
8
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
439 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
440
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
441 **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
442
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
443 .. 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
444 :width: 558
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
445 :height: 412
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
446
8
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
447 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
448
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
449 **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
450
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
451 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
452
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
453 * 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
454 * `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
455 * `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
456 * `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
457 * 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
458 * 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
459 * 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
460
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
461 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
462
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
463 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
464 # 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
465 # 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
466 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
467 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
468 # 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
469 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
470 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
471 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
472 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
473 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
474 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
475 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
476 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
477 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
478 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
479 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
480 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
481 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
482 # 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
483 # 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
484 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
485 # 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
486 # 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
487 # 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
488 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
489 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
490 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
491 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
492 # 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
493 # 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
494 # 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
495 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
496 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
497 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
498 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
499 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
500 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
501 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
502 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
503 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
504 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
505
8
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
506 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
507
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
508 Using reference also produces an **Alignment viewer**:
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
509
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
510 .. 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
511 :width: 515
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
512 :height: 395
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
513
8
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
514 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
515
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
516 ]]>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
517 </help>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
518
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
519 <citations>
8
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
520 <citation type="doi">10.1093/bioinformatics/bty266</citation>
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
521 <citation type="doi">10.1093/bioinformatics/btw379</citation>
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
522 <citation type="doi">10.1093/bioinformatics/btv697</citation>
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
523 <citation type="doi">10.1093/bioinformatics/btt086</citation>
0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
524 </citations>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
525 </tool>