Mercurial > repos > iuc > quast
changeset 2:2f581f956e1c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 930a43568ac0d4d32dde38a56fbb0b826f8f591b
| author | iuc |
|---|---|
| date | Fri, 04 Nov 2016 05:06:15 -0400 |
| parents | 0edbf19cf5eb |
| children | 6fcbee531de6 |
| files | quast.xml test-data/Quast_report.tex test-data/Quast_report.tsv test-data/Quast_report.txt |
| diffstat | 4 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/quast.xml Wed Nov 02 09:42:45 2016 -0400 +++ b/quast.xml Fri Nov 04 05:06:15 2016 -0400 @@ -11,6 +11,7 @@ </stdio> <command> <![CDATA[ + #import re quast -o outputdir #if $gene_selection == "eukaryote": @@ -32,7 +33,8 @@ #end if --min-contig $min_contig -l - #set names = ','.join( ['"'+str( $x.input.element_identifier)+'"' for $x in $files ]) + #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.input.element_identifier))+'"' for $x in $files ]) + $names --contig-thresholds $threshold_contig #for $k in $files:
--- a/test-data/Quast_report.tex Wed Nov 02 09:42:45 2016 -0400 +++ b/test-data/Quast_report.tex Fri Nov 04 05:06:15 2016 -0400 @@ -5,7 +5,7 @@ \caption{All statistics are based on contigs of size $\geq$ 500 bp, unless otherwise noted (e.g., "\# contigs ($\geq$ 0 bp)" and "Total length ($\geq$ 0 bp)" include all contigs).} \begin{tabular}{|l*{1}{|r}|} \hline -Assembly & contigs\_1.fasta \\ \hline +Assembly & contigs\_1\_fasta \\ \hline \# contigs ($\geq$ 0 bp) & 3 \\ \hline \# contigs ($\geq$ 1000 bp) & 3 \\ \hline Total length ($\geq$ 0 bp) & 6710 \\ \hline
--- a/test-data/Quast_report.tsv Wed Nov 02 09:42:45 2016 -0400 +++ b/test-data/Quast_report.tsv Fri Nov 04 05:06:15 2016 -0400 @@ -1,4 +1,4 @@ -Assembly contigs_1.fasta +Assembly contigs_1_fasta # contigs (>= 0 bp) 3 # contigs (>= 1000 bp) 3 Total length (>= 0 bp) 6710
--- a/test-data/Quast_report.txt Wed Nov 02 09:42:45 2016 -0400 +++ b/test-data/Quast_report.txt Fri Nov 04 05:06:15 2016 -0400 @@ -1,6 +1,6 @@ All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs). -Assembly contigs_1.fasta +Assembly contigs_1_fasta # contigs (>= 0 bp) 3 # contigs (>= 1000 bp) 3 Total length (>= 0 bp) 6710