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comparison quast.xml @ 5:844452fe09f8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
author iuc
date Tue, 04 Dec 2018 06:48:42 -0500
parents d90201633fb9
children bf2c7b30dfb6
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4:d90201633fb9 5:844452fe09f8
1 <tool id="quast" name="Quast" version="4.6.3" > 1 <tool id="quast" name="Quast" version="5.0.2" >
2 <description>Genome assembly Quality</description> 2 <description>Genome assembly Quality</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.6.3">quast</requirement> 4 <requirement type="package" version="5.0.2">quast</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <command detect_errors="exit_code">
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[ 7 <![CDATA[
14 #import re 8 #import re
15 quast 9 quast
16 --threads \${GALAXY_SLOTS:-4} 10 --threads \${GALAXY_SLOTS:-4}
17 -o outputdir 11 -o outputdir
18 #if $gene_selection == "eukaryote": 12 #if $gene_selection == "eukaryote":
19 --eukaryote 13 --eukaryote
20 #else if $gene_selection == "metagenes": 14 #else if $gene_selection == "metagenes":
21 --meta 15 --meta
22 #end if 16 #end if
23 #if $input_ref: 17 $large
24 -R '$input_ref' 18 #if $input_ref:
25 #if $input_operon: 19 -R '$input_ref'
26 -O '$input_operon' 20 #if $input_operon:
27 #end if 21 -O '$input_operon'
28 #if $annot: 22 #end if
29 -G '$annot' 23 #if $annot:
30 #end if 24 -g '$annot'
31 #end if 25 #end if
32 #if $input_size: 26 #end if
33 --est-ref-size $input_size 27 #if $input_size:
34 #end if 28 --est-ref-size $input_size
35 --min-contig $min_contig 29 #end if
36 -l 30 --min-contig $min_contig
37 #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.element_identifier))+'"' for $x in $input ]) 31 -l
38 32 #set names = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $input ])
39 $names 33
40 --contig-thresholds $threshold_contig 34 '$names'
41 #for $k in $input: 35 --contig-thresholds $threshold_contig
42 $k 36 #for $k in $input:
43 #end for 37 $k
44 && 38 #end for
45 mv outputdir/report.tsv '$quast_tsv' && 39 && mkdir '$report_html.files_path'
46 ## The sed string below removes non-functional "Main menu" button from the viewer 40 && cp outputdir/*.html '$report_html.files_path'
47 sed '\:<div class="btn btn-inverse" id="to_main_menu_button">:,\:</div>:d' outputdir/icarus_viewers/contig_size_viewer.html > '$contig_size_viewer' && 41 #if str($input_ref):
48 #if $input_ref: 42 && cp -R outputdir/icarus_viewers '$report_html.files_path'
49 ## The sed string below removes non-functional "Main menu" button from the viewer 43 #end if
50 sed '\:<div class="btn btn-inverse" id="to_main_menu_button">:,\:</div>:d' outputdir/icarus_viewers/alignment_viewer.html > '$alignment_viewer' &&
51 #end if
52 ## The sed string below removes non-functional link from the report page
53 sed "\:<div id='icarus-json'>:,\:</div>:d" outputdir/report.html > '$report_html' &&
54 mv outputdir/report.pdf '$report_pdf' &&
55 mv outputdir/contigs_reports/misassemblies_report.tsv '$mis_ass_tsv' &&
56 mv outputdir/contigs_reports/unaligned_report.tsv '$unalign_tsv' &&
57 mv outputdir/quast.log '$log_txt'
58 ]]> 44 ]]>
59 </command> 45 </command>
60 <inputs> 46 <inputs>
61 <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file" multiple="True"/> 47 <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file" multiple="True"/>
62 <param name="type_file" type="select" label="Type of data"> 48 <param name="type_file" type="select" label="Type of data">
63 <option value="contig">Contig</option> 49 <option value="contig">Contig</option>
64 <option value="scaffold">Scaffold</option> 50 <option value="scaffold">Scaffold</option>
65 </param> 51 </param>
66 <param name="input_size" type="integer" label="Size of reference genome" optional="True" argument="--est-ref-size" 52 <param name="input_size" type="integer" label="Size of reference genome" optional="True" argument="--est-ref-size"
67 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 "/> 53 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 "/>
54 <param argument="--large" type="boolean" truevalue="--large" falsevalue="" label="Run quast in --large mode for large genomes" help="Uses minimap2 aligner, improves transposable element handling and alignment thresholds"/>
68 <param name="input_ref" type="data" format="fasta" label="Reference genome" optional="True" argument="-R" 55 <param name="input_ref" type="data" format="fasta" label="Reference genome" optional="True" argument="-R"
69 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."/> 56 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."/>
70 <param name="annot" type="data" format="gff, gff3, bed" label="Gene Annotations" optional="True" argument="-G" 57 <param name="annot" type="data" format="gff, gff3, bed" label="Gene Annotations" optional="True" argument="-G"
71 help="Gene coordinates for the reference genome (only relevant if the reference genome is used). "/> 58 help="Gene coordinates for the reference genome (only relevant if the reference genome is used). "/>
72 <param name="input_operon" type="data" format="gff, gff3, bed" label="Operon Annotations" optional="True" argument="-O" help="Operon coordinates for the reference genome (only relevant if the reference genome is used)."/> 59 <param name="input_operon" type="data" format="gff, gff3, bed" label="Operon Annotations" optional="True" argument="-O" help="Operon coordinates for the reference genome (only relevant if the reference genome is used)."/>
78 help="Set the lower threshold for a contig length. Shorter contigs won't be taken into account [default is 500]"/> 65 help="Set the lower threshold for a contig length. Shorter contigs won't be taken into account [default is 500]"/>
79 <param name="threshold_contig" type="text" value="0,1000" label="Thresholds" argument="--contig-thresholds" 66 <param name="threshold_contig" type="text" value="0,1000" label="Thresholds" argument="--contig-thresholds"
80 help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.[default is 0,1000]"/> 67 help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.[default is 0,1000]"/>
81 </inputs> 68 </inputs>
82 <outputs> 69 <outputs>
83 <data format="txt" name="log_txt" label="Quast: Log" /> 70 <data format="txt" name="log_txt" label="Quast: Log" from_work_dir="outputdir/quast.log"/>
84 <data format="tabular" name="mis_ass_tsv" label="Quast: Misassemblies"> 71 <data format="tabular" name="mis_ass_tsv" label="Quast: Misassemblies" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
85 <filter>input_ref is not None</filter> 72 <filter>input_ref is not None</filter>
86 </data> 73 </data>
87 <data format="tabular" name="unalign_tsv" label="Quast: Unaligned contigs"> 74 <data format="tabular" name="unalign_tsv" label="Quast: Unaligned contigs" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv">
88 <filter>input_ref is not None</filter> 75 <filter>input_ref is not None</filter>
89 </data> 76 </data>
90 <data format="html" name="contig_size_viewer" label="Quast: Contig view"/> 77 <data format="tabular" name="quast_tsv" label="Quast: Report (tabulal)" from_work_dir="outputdir/report.tsv"/>
91 <data format="html" name="alignment_viewer" label="Quast: Alignment view"> 78 <data format="html" name="report_html" label="Quast: Report (HTML)" from_work_dir="outputdir/report.html"/>
92 <filter>input_ref is not None</filter> 79 <data format="pdf" name="report_pdf" label="Quast: Report (PDF)" from_work_dir="outputdir/report.pdf"/>
93 </data>
94 <data format="tabular" name="quast_tsv" label="Quast: Report (tabulal)"/>
95 <data format="html" name="report_html" label="Quast: Report (HTML)"/>
96 <data format="pdf" name="report_pdf" label="Quast: Report (PDF)"/>
97 </outputs> 80 </outputs>
98 <tests> 81 <tests>
99 <test> 82 <test>
100 <!-- Test with reference and genes annotations --> 83 <!-- Test with reference and genes annotations -->
101 <param name="input" value="contigs2.fna,contigs1.fna"/> 84 <param name="input" value="contigs2.fna,contigs1.fna"/>
102 <param name="input_ref" value="reference.fna"/> 85 <param name="input_ref" value="reference.fna"/>
103 <param name="type_file" value="contig"/> 86 <param name="type_file" value="contig"/>
104 <param name="annot" value="genes.gff"/> 87 <param name="annot" value="genes.gff"/>
105 <param name="gene_selection" value="prokaryotes"/> 88 <param name="gene_selection" value="prokaryotes"/>
89 <param name="large" value="true"/>
106 <output name="quast_tsv" file="test1_output.tsv" lines_diff="4"/> 90 <output name="quast_tsv" file="test1_output.tsv" lines_diff="4"/>
107 </test> 91 </test>
108 <test> 92 <test>
109 <!-- Test without reference --> 93 <!-- Test without reference -->
110 <param name="input" value="contigs2.fna,contigs1.fna"/> 94 <param name="input" value="contigs2.fna,contigs1.fna"/>
111 <param name="type_file" value="contig"/> 95 <param name="type_file" value="contig"/>
112 <output name="quast_tsv" file="test2_output.tsv" lines_diff="4"/> 96 <output name="quast_tsv" file="test2_output.tsv" lines_diff="4"/>
97 <output name="report_html" file="test2_report.html" lines_diff="50"/>
98 <output name="report_pdf" file="test2_report.pdf" compare="sim_size"/>
113 </test> 99 </test>
114 </tests> 100 </tests>
115 <help> 101 <help>
116 <![CDATA[ 102 <![CDATA[
117 **What it does** 103 **What it does**