Mercurial > repos > iuc > quast

comparison quast.xml @ 3:6fcbee531de6 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 cd130fcce3254cddb9a3f501f43feaa3f37c1b67
author iuc
date Fri, 29 Sep 2017 05:51:26 -0400
parents 2f581f956e1c
children 0834c823d4b9
comparison
equal deleted inserted replaced
2:2f581f956e1c 3:6fcbee531de6
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