Mercurial > repos > iuc > quast
comparison quast.xml @ 5:81df4950d65b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
author | iuc |
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date | Tue, 04 Dec 2018 06:49:05 -0500 |
parents | 0834c823d4b9 |
children | f30d03867854 |
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4:0834c823d4b9 | 5:81df4950d65b |
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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** |