Mercurial > repos > iuc > quast
changeset 1:0edbf19cf5eb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9cf2e1454bf23a11ca0e7eeb26b4eaa446832bf8
| author | iuc |
|---|---|
| date | Wed, 02 Nov 2016 09:42:45 -0400 |
| parents | 736d51130b41 |
| children | 2f581f956e1c |
| files | README.md README.txt quast.xml test-data/Quast_report.tex test-data/Quast_report.tsv test-data/Quast_report.txt |
| diffstat | 6 files changed, 42 insertions(+), 39 deletions(-) [+] |
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--- a/README.md Tue Sep 13 14:43:54 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -**Tool Information** - -- QUAST Tool v4.1: - + Release Date: May 2016 - + URL: http://bioinf.spbau.ru/quast - + Source URL: https://downloads.sourceforge.net/project/quast/quast-4.1.tar.gz - ------ - -**QUAST Galaxy Wrapper Author and Contact Information** - -+ Delphine Lariviere -+ Galaxy Team -+ Email: delphine.lariviere@galaxyproject.org -+ Nekrutenko's Lab, Pennsylvania State University, State College, PA, USA - - -- From the wrapper of : - + Jacob Jablonski - + AAFC-MBB Team - + Email: mbb@agr.gc.ca - + Agriculture and Agri-foods Canada, Ottawa, ON, Canada
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Wed Nov 02 09:42:45 2016 -0400 @@ -0,0 +1,22 @@ +**Tool Information** + +- QUAST Tool v4.1: + + Release Date: May 2016 + + URL: http://bioinf.spbau.ru/quast + + Source URL: https://downloads.sourceforge.net/project/quast/quast-4.1.tar.gz + +----- + +**QUAST Galaxy Wrapper Author and Contact Information** + ++ Delphine Lariviere ++ Galaxy Team ++ Email: delphine.lariviere@galaxyproject.org ++ Nekrutenko's Lab, Pennsylvania State University, State College, PA, USA + + +- From the wrapper of : + + Jacob Jablonski + + AAFC-MBB Team + + Email: mbb@agr.gc.ca + + Agriculture and Agri-foods Canada, Ottawa, ON, Canada
--- a/quast.xml Tue Sep 13 14:43:54 2016 -0400 +++ b/quast.xml Wed Nov 02 09:42:45 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="quast" name="Quast" version="4.1" > +<tool id="quast" name="Quast" version="4.1.1" > <description>Genome assembly Quality</description> <requirements> <requirement type="package" version="4.1">quast</requirement> @@ -31,6 +31,9 @@ --est-ref-size $input_size #end if --min-contig $min_contig + -l + #set names = ','.join( ['"'+str( $x.input.element_identifier)+'"' for $x in $files ]) + $names --contig-thresholds $threshold_contig #for $k in $files: #if $k.type_file == "scaffold":
--- a/test-data/Quast_report.tex Tue Sep 13 14:43:54 2016 -0400 +++ b/test-data/Quast_report.tex Wed Nov 02 09:42:45 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 \\ \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 Tue Sep 13 14:43:54 2016 -0400 +++ b/test-data/Quast_report.tsv Wed Nov 02 09:42:45 2016 -0400 @@ -1,4 +1,4 @@ -Assembly contigs_1 +Assembly contigs_1.fasta # contigs (>= 0 bp) 3 # contigs (>= 1000 bp) 3 Total length (>= 0 bp) 6710
--- a/test-data/Quast_report.txt Tue Sep 13 14:43:54 2016 -0400 +++ b/test-data/Quast_report.txt Wed Nov 02 09:42:45 2016 -0400 @@ -1,16 +1,16 @@ 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 -# contigs (>= 0 bp) 3 -# contigs (>= 1000 bp) 3 -Total length (>= 0 bp) 6710 -Total length (>= 1000 bp) 6710 -# contigs 3 -Largest contig 3980 -Total length 6710 -GC (%) 51.28 -N50 3980 -N75 1610 -L50 1 -L75 2 -# N's per 100 kbp 0.00 +Assembly contigs_1.fasta +# contigs (>= 0 bp) 3 +# contigs (>= 1000 bp) 3 +Total length (>= 0 bp) 6710 +Total length (>= 1000 bp) 6710 +# contigs 3 +Largest contig 3980 +Total length 6710 +GC (%) 51.28 +N50 3980 +N75 1610 +L50 1 +L75 2 +# N's per 100 kbp 0.00