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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
author iuc
date Tue, 13 Sep 2016 14:43:54 -0400
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1 <tool id="quast" name="Quast" version="4.1" >
2 <description>Genome assembly Quality</description>
3 <requirements>
4 <requirement type="package" version="4.1">quast</requirement>
5 </requirements>
6 <stdio>
7 <regex match="ERROR! exception caught!"
8 source="both"
9 level="fatal"
10 description="Something went wrong. Check the following errors : No labels..." />
11 </stdio>
12 <command>
13 <![CDATA[
14 quast
15 -o outputdir
16 #if $gene_selection == "eukaryote":
17 --eukaryote
18 #else if $gene_selection == "metagenes":
19 --meta
20 #end if
21 #if $input_ref:
22 -R '$input_ref'
23 #if $input_operon:
24 -O '$input_operon'
25 #end if
26 #if $annot:
27 -G '$annot'
28 #end if
29 #end if
30 #if $input_size:
31 --est-ref-size $input_size
32 #end if
33 --min-contig $min_contig
34 --contig-thresholds $threshold_contig
35 #for $k in $files:
36 #if $k.type_file == "scaffold":
37 -s
38 #end if
39 $k.input
40 #end for
41 &&
42 mv outputdir/report.txt '$quast_out' &&
43 mv outputdir/report.tsv '$quast_tsv' &&
44 mv outputdir/report.tex '$quast_tex' &&
45 mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' &&
46 mv outputdir/report.html '$report_html'
47 ]]>
48 </command>
49 <inputs>
50 <repeat name="files" title="Input assembly files" min="1">
51 <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file"/>
52 <param name="type_file" type="select" label="Type of data">
53 <option value="contig">Contig</option>
54 <option value="scaffold">Scaffold</option>
55 </param>
56 </repeat>
57 <param name="input_size" type="integer" label="Size of reference genome" optional="True" argument="--est-ref-size"
58 help="Estimated reference genome size (in bp) for computing NGx statistics, if known. This value will be used only if a reference genome file is not specified "/>
59 <param name="input_ref" type="data" format="fasta" label="Reference File" optional="True" argument="-R"
60 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."/>
61 <param name="annot" type="data" format="txt" label="Gene Annotations" optional="True" argument="-G"
62 help="File with gene positions in the reference genome. "/>
63 <param name="input_operon" type="data" format="txt" label="Operon Annotations" optional="True" argument="-O"
64 help="File with operon positions in the reference genome"/>
65 <param name="gene_selection" type="select" label="Type of organism">
66 <option value="prokaryotes">Prokaryotes</option>
67 <option value="eukaryote">Eukaryote</option>
68 <option value="metagenes">Metagenomes</option>
69 </param>
70 <param name="min_contig" type="integer" value="500" label="Lower Threshold" argument="--min-contig"
71 help="Set the lower threshold for a contig length. Shorter contigs won't be taken into account (default is 500)"/>
72 <param name="threshold_contig" type="text" value="0,1000" label="Thresholds" argument="--contig-thresholds"
73 help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.(default is 0,1000)"/>
74 </inputs>
75 <outputs>
76 <data format="txt" name="quast_out" label="Quast report.txt" from_work_dir="Quast_report.txt"/>
77 <data format="tsv" name="quast_tsv" label="Quast report.tsv" from_work_dir="Quast_report.tsv"/>
78 <data format="tex" name="quast_tex" label="Quast report.tex" from_work_dir="Quast_report.tex"/>
79 <data format="html" name="icarus" label="Icarus Contig size viewer" from_work_dir="Icarus.html"/>
80 <data format="html" name="report_html" label="Quast report.html" from_work_dir="Quast_report.html"/>
81 </outputs>
82 <tests>
83 <test>
84 <param name="input" value="contigs_1.fasta"/>
85 <param name="input.type_file" value="contig"/>
86 <param name="gene_selection" value="prokaryotes"/>
87 <output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/>
88 </test>
89 </tests>
90 <help>
91 <![CDATA[
92 **Description**
93
94 Galaxy tool wrapper for the QUAST tool. Quast stands for QUality ASsessment Tool. It evaluates genome assemblies by computing various metrics.
95
96 -----
97
98 **Inputs and Outputs**
99
100 - Input:
101 + The tool accepts assemblies and references in FASTA format.
102 + The tool accepts annotation and operon files in:
103 + GFF, versions 2 and 3 (note: feature/type field should be either "gene" or "operon")
104 + the format used by NCBI for genes ("Summary (text)");
105 + four tab-separated columns: sequence name, gene/operon id, start position, end position
106
107 - Output:
108 + An assessment summary in plain text format
109 + An assessment summary in tabulation separated values format
110 + An assessment summary in LateX format
111 + An assessment summary in HTML format
112 + An HTML view of contig sizes wit Icarus
113
114
115 ]]>
116 </help>
117
118 <citations>
119 <citation type="bibtex">@ARTICLE{a1,
120 author = {Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler},
121 title = {QUAST: quality assessment tool for genomce assemblies, Bioinformatics (2013) 29 (8): 1072-1075}
122 }</citation>
123 <citation type="bibtex">@misc{quast41,
124 title = {{Quast} v4.1},
125 howpublished = {http://bioinf.spbau.ru/quast},
126 note = {Released May 2016}}
127 }</citation>
128 </citations>
129 </tool>