Mercurial > repos > iuc > quast
comparison quast.xml @ 3:6fcbee531de6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
author | iuc |
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date | Fri, 29 Sep 2017 05:51:26 -0400 |
parents | 2f581f956e1c |
children | 0834c823d4b9 |
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2:2f581f956e1c | 3:6fcbee531de6 |
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1 <tool id="quast" name="Quast" version="4.1.1" > | 1 <tool id="quast" name="Quast" version="4.5" > |
2 <description>Genome assembly Quality</description> | 2 <description>Genome assembly Quality</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="4.1">quast</requirement> | 4 <requirement type="package" version="4.5">quast</requirement> |
5 </requirements> | 5 </requirements> |
6 <stdio> | 6 <stdio> |
7 <regex match="ERROR! exception caught!" | 7 <regex match="ERROR! exception caught!" |
8 source="both" | 8 source="both" |
9 level="fatal" | 9 level="fatal" |
11 </stdio> | 11 </stdio> |
12 <command> | 12 <command> |
13 <![CDATA[ | 13 <![CDATA[ |
14 #import re | 14 #import re |
15 quast | 15 quast |
16 --threads \${GALAXY_SLOTS:-4} | |
16 -o outputdir | 17 -o outputdir |
17 #if $gene_selection == "eukaryote": | 18 #if $gene_selection == "eukaryote": |
18 --eukaryote | 19 --eukaryote |
19 #else if $gene_selection == "metagenes": | 20 #else if $gene_selection == "metagenes": |
20 --meta | 21 --meta |
32 --est-ref-size $input_size | 33 --est-ref-size $input_size |
33 #end if | 34 #end if |
34 --min-contig $min_contig | 35 --min-contig $min_contig |
35 -l | 36 -l |
36 #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.input.element_identifier))+'"' for $x in $files ]) | 37 #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.input.element_identifier))+'"' for $x in $files ]) |
37 | 38 |
38 $names | 39 $names |
39 --contig-thresholds $threshold_contig | 40 --contig-thresholds $threshold_contig |
40 #for $k in $files: | 41 #for $k in $files: |
41 #if $k.type_file == "scaffold": | 42 #if $k.type_file == "scaffold": |
42 -s | 43 -s |
46 && | 47 && |
47 mv outputdir/report.txt '$quast_out' && | 48 mv outputdir/report.txt '$quast_out' && |
48 mv outputdir/report.tsv '$quast_tsv' && | 49 mv outputdir/report.tsv '$quast_tsv' && |
49 mv outputdir/report.tex '$quast_tex' && | 50 mv outputdir/report.tex '$quast_tex' && |
50 mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' && | 51 mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' && |
51 mv outputdir/report.html '$report_html' | 52 mv outputdir/report.html '$report_html' |
52 ]]> | 53 ]]> |
53 </command> | 54 </command> |
54 <inputs> | 55 <inputs> |
55 <repeat name="files" title="Input assembly files" min="1"> | 56 <repeat name="files" title="Input assembly files" min="1"> |
56 <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file"/> | 57 <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file"/> |
89 <param name="input" value="contigs_1.fasta"/> | 90 <param name="input" value="contigs_1.fasta"/> |
90 <param name="input.type_file" value="contig"/> | 91 <param name="input.type_file" value="contig"/> |
91 <param name="gene_selection" value="prokaryotes"/> | 92 <param name="gene_selection" value="prokaryotes"/> |
92 <output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/> | 93 <output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/> |
93 </test> | 94 </test> |
95 <test> | |
96 <param name="input" value="contigs_1.fasta"/> | |
97 <param name="input.type_file" value="contig"/> | |
98 <param name="input_ref" value="NC000913.3_1-6650.fasta"/> | |
99 <param name="gene_selection" value="prokaryotes"/> | |
100 <output name="quast_tsv" file="Quast_report_withref.tsv" lines_diff="4"/> | |
101 </test> | |
102 <test> | |
103 <param name="input" value="contigs_1.fasta"/> | |
104 <param name="input.type_file" value="contig"/> | |
105 <param name="input_ref" value="NC000913.3_1-6650.fasta"/> | |
106 <param name="annot" value="NC000913.3_1-6650.gff"/> | |
107 <param name="gene_selection" value="prokaryotes"/> | |
108 <output name="quast_tsv" file="Quast_report_withref_withgenes.tsv" lines_diff="4"/> | |
109 </test> | |
94 </tests> | 110 </tests> |
95 <help> | 111 <help> |
96 <![CDATA[ | 112 <![CDATA[ |
97 **Description** | 113 **Description** |
98 | 114 |