| Next changeset 1:0edbf19cf5eb (2016-11-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09 |
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README.md quast.xml test-data/Quast_report.tex test-data/Quast_report.tsv test-data/Quast_report.txt test-data/contigs_1.fasta |
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| diff -r 000000000000 -r 736d51130b41 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Sep 13 14:43:54 2016 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r 736d51130b41 quast.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/quast.xml Tue Sep 13 14:43:54 2016 -0400 |
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| @@ -0,0 +1,129 @@ +<tool id="quast" name="Quast" version="4.1" > + <description>Genome assembly Quality</description> + <requirements> + <requirement type="package" version="4.1">quast</requirement> + </requirements> + <stdio> + <regex match="ERROR! exception caught!" + source="both" + level="fatal" + description="Something went wrong. Check the following errors : No labels..." /> + </stdio> + <command> + <![CDATA[ + quast + -o outputdir + #if $gene_selection == "eukaryote": + --eukaryote + #else if $gene_selection == "metagenes": + --meta + #end if + #if $input_ref: + -R '$input_ref' + #if $input_operon: + -O '$input_operon' + #end if + #if $annot: + -G '$annot' + #end if + #end if + #if $input_size: + --est-ref-size $input_size + #end if + --min-contig $min_contig + --contig-thresholds $threshold_contig + #for $k in $files: + #if $k.type_file == "scaffold": + -s + #end if + $k.input + #end for + && + mv outputdir/report.txt '$quast_out' && + mv outputdir/report.tsv '$quast_tsv' && + mv outputdir/report.tex '$quast_tex' && + mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' && + mv outputdir/report.html '$report_html' + ]]> + </command> + <inputs> + <repeat name="files" title="Input assembly files" min="1"> + <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file"/> + <param name="type_file" type="select" label="Type of data"> + <option value="contig">Contig</option> + <option value="scaffold">Scaffold</option> + </param> + </repeat> + <param name="input_size" type="integer" label="Size of reference genome" optional="True" argument="--est-ref-size" + 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 "/> + <param name="input_ref" type="data" format="fasta" label="Reference File" optional="True" argument="-R" + 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."/> + <param name="annot" type="data" format="txt" label="Gene Annotations" optional="True" argument="-G" + help="File with gene positions in the reference genome. "/> + <param name="input_operon" type="data" format="txt" label="Operon Annotations" optional="True" argument="-O" + help="File with operon positions in the reference genome"/> + <param name="gene_selection" type="select" label="Type of organism"> + <option value="prokaryotes">Prokaryotes</option> + <option value="eukaryote">Eukaryote</option> + <option value="metagenes">Metagenomes</option> + </param> + <param name="min_contig" type="integer" value="500" label="Lower Threshold" argument="--min-contig" + help="Set the lower threshold for a contig length. Shorter contigs won't be taken into account (default is 500)"/> + <param name="threshold_contig" type="text" value="0,1000" label="Thresholds" argument="--contig-thresholds" + help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.(default is 0,1000)"/> + </inputs> + <outputs> + <data format="txt" name="quast_out" label="Quast report.txt" from_work_dir="Quast_report.txt"/> + <data format="tsv" name="quast_tsv" label="Quast report.tsv" from_work_dir="Quast_report.tsv"/> + <data format="tex" name="quast_tex" label="Quast report.tex" from_work_dir="Quast_report.tex"/> + <data format="html" name="icarus" label="Icarus Contig size viewer" from_work_dir="Icarus.html"/> + <data format="html" name="report_html" label="Quast report.html" from_work_dir="Quast_report.html"/> + </outputs> + <tests> + <test> + <param name="input" value="contigs_1.fasta"/> + <param name="input.type_file" value="contig"/> + <param name="gene_selection" value="prokaryotes"/> + <output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/> + </test> + </tests> + <help> +<![CDATA[ +**Description** + +Galaxy tool wrapper for the QUAST tool. Quast stands for QUality ASsessment Tool. It evaluates genome assemblies by computing various metrics. + +----- + +**Inputs and Outputs** + +- Input: + + The tool accepts assemblies and references in FASTA format. + + The tool accepts annotation and operon files in: + + GFF, versions 2 and 3 (note: feature/type field should be either "gene" or "operon") + + the format used by NCBI for genes ("Summary (text)"); + + four tab-separated columns: sequence name, gene/operon id, start position, end position + +- Output: + + An assessment summary in plain text format + + An assessment summary in tabulation separated values format + + An assessment summary in LateX format + + An assessment summary in HTML format + + An HTML view of contig sizes wit Icarus + + + ]]> + </help> + + <citations> + <citation type="bibtex">@ARTICLE{a1, + author = {Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler}, + title = {QUAST: quality assessment tool for genomce assemblies, Bioinformatics (2013) 29 (8): 1072-1075} + }</citation> + <citation type="bibtex">@misc{quast41, + title = {{Quast} v4.1}, + howpublished = {http://bioinf.spbau.ru/quast}, + note = {Released May 2016}} + }</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 736d51130b41 test-data/Quast_report.tex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Quast_report.tex Tue Sep 13 14:43:54 2016 -0400 |
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| @@ -0,0 +1,25 @@ +\documentclass[12pt,a4paper]{article} +\begin{document} +\begin{table}[ht] +\begin{center} +\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 +\# contigs ($\geq$ 0 bp) & 3 \\ \hline +\# contigs ($\geq$ 1000 bp) & 3 \\ \hline +Total length ($\geq$ 0 bp) & 6710 \\ \hline +Total length ($\geq$ 1000 bp) & 6710 \\ \hline +\# contigs & 3 \\ \hline +Largest contig & 3980 \\ \hline +Total length & 6710 \\ \hline +GC (\%) & 51.28 \\ \hline +N50 & 3980 \\ \hline +N75 & 1610 \\ \hline +L50 & 1 \\ \hline +L75 & 2 \\ \hline +\# N's per 100 kbp & 0.00 \\ \hline +\end{tabular} +\end{center} +\end{table} +\end{document} |
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| diff -r 000000000000 -r 736d51130b41 test-data/Quast_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Quast_report.tsv Tue Sep 13 14:43:54 2016 -0400 |
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| @@ -0,0 +1,14 @@ +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 |
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| diff -r 000000000000 -r 736d51130b41 test-data/Quast_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Quast_report.txt Tue Sep 13 14:43:54 2016 -0400 |
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| @@ -0,0 +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 |
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| diff -r 000000000000 -r 736d51130b41 test-data/contigs_1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs_1.fasta Tue Sep 13 14:43:54 2016 -0400 |
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| @@ -0,0 +1,99 @@ +>contig1 +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC +TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA +TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC +ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG +CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA +GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC +AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG +AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT +GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT +GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC +TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT +TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT +GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG +CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC +TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT +CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG +>contig2 +ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG +GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACA +TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG +GAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGA +AAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGC +CGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC +TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTG +GATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT +TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACG +CTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTA +AACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCT +GCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC +TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG +ATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGA +AAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGC +AATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC +ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG +TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA +CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAG +CGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTT +CGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC +GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTAC +GACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGC +>contig3 +GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAA +ATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGT +TAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAA +TCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATT +CTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATC +TGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT +CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAA +AGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCAT +CGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATC +TATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTC +CCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCG +ACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC +GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACATCACCGCTAA +ATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTAC +GTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCA +TTGACTGCAAACTTAACGCTGCTCGTAGCGTTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCA +AAGAAGTAACCTTCGCTATTAAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAAC +GACTCATCAGACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG +GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTCATCTGACGCC +AGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTTGTTGGTGATGATATCTCCCC +AGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACGGATCCCCATTTCCAGACGATAAGGCTGCAT +TAAATCGAGCGGGCGGAGTACGCCATACAAGCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAA +TCGTCTTCGCTGAAGGTTTCGGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGC +GGGCATTCGCCGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC +GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAACTGCTGGGAA +TTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTGGTAATCAAGCGTTTTCGCAG +GTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATTTATGCCGACTTTAGCAAAAAATGAGAATGA +GTTGATCGATAGTTGTGATTACTCCTGCGAAACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATA +TCCGGATAACGCAATGGATCAAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA +CTTCTGCGTAGCATACATGAGGTTTTGTATAAAAATGGCGGGCGATATCAACGCAGTGTCAGAAATCCGA +AACAGTCTCGCCTGGCGATAACCGTCTTGTCGGCGGTTGCGCTGACGTTGCGTCGTGATATCATCAGGGC +AGACCGGTTACATCCCCCTAACAAGCTGTTTAAAGAGAAATACTATCATGACGGACAAATTGACCTCCCT +TCGTCAGTACACCACCGTAGTGGCCGACACTGGGGACATCGCGGCAATGAAGCTGTATCAACCGCAGGAT +GCCACAACCAACCCTTCTCTCATTCTTAACGCAGCGCAGATTCCGGAATACCGTAAGTTGATTGATGATG +CTGTCGCCTGGGCGAAACAGCAGAGCAACGATCGCGCGCAGCAGATCGTGGACGCGACCGACAAACTGGC +AGTAAATATTGGTCTGGAAATCCTGAAACTGGTTCCGGGCCGTATCTCAACTGAAGTTGATGCGCGTCTT +TCCTATGACACCGAAGCGTCAATTGCGAAAGCAAAACGCCTGATCAAACTCTACAACGATGCTGGTATTA +GCAACGATCGTATTCTGATCAAACTGGCTTCTACCTGGCAGGGTATCCGTGCTGCAGAACAGCTGGAAAA +AGAAGGCATCAACTGTAACCTGACCCTGCTGTTCTCCTTCGCTCAGGCTCGTGCTTGTGCGGAAGCGGGC +GTGTTCCTGATCTCGCCGTTTGTTGGCCGTATTCTTGACTGGTACAAAGCGAATACCGATAAGAAAGAGT +ACGCTCCGGCAGAAGATCCGGGCGTGGTTTCTGTATCTGAAATCTACCAGTACTACAAAGAGCACGGTTA +TGAAACCGTGGTTATGGGCGCAAGCTTCCGTAACATCGGCGAAATTCTGGAACTGGCAGGCTGCGACCGT +CTGACCATCGCACCGGCACTGCTGAAAGAGCTGGCGGAGAGCGAAGGGGCTATCGAACGTAAACTGTCTT +ACACCGGCGAAGTGAAAGCGCGTCCGGCGCGTATCACTGAGTCCGAGTTCCTGTGGCAGCACAACCAGGA +TCCAATGGCAGTAGATAAACTGGCGGAAGGTATCCGTAAGTTTGCTATTGACCAGGAAAAACTGGAAAAA +ATGATCGGCGATCTGCTGTAATCATTCTTAGCGTGACCGGGAAGTCGGTCACGCTACCTCTTCTGAAGCC +TGTCTGTCACTCCCTTCGCAGTGTATCATTCTGTTTAACGAGACTGTTTAAACGGAAAAATCTTGATGAA +TACTTTACGTATTGGCTTAGTTTCCATCTCTGATCGCGCATCCAGCGGCGTTTATCAGGATAAAGGCATC +CCTGCGCTGGAAGAATGGCTGACATCGGCGCTAACCACGCCGTTTGAACTGGAAACCCGCTTAATCCCCG +ATGAGCAGGCGATCATCGAGCAAACGTTGTGTGAGCTGGTGGATGAAATGAGTTGCCATCTGGTGCTCAC +CACGGGCGGAACTGGCCCGGCGCGTCGTGACGTAACGCCCGATGCGACGCTGGCAGTAGCGGACCGCGAG +ATGCCTGGCTTTGGTGAACAGATGCGCCAGATCAGCCTGCATTTTGTACCAACTGCGATCCTTTCGCGTC +AGGTGGGCGTGATTCGCAAACAGGCGCTGATCCTTAACTTACCCGGTCAGCCGAAGTCTATTAAAGAGAC +GCTGGAAGGTGTGAAGGACGCTGAGGGTAACGTTGTGGTACACGGTATTTTTGCCAGCGTACCGTACTGC +ATTCAGTTGCTGGAAGGGCCATACGTTGAAACGGCACCGGAAGTGGTTGCAGCATTCAGACCGAAGAGTG +CAAGACGCGACGTTAGCGAATAAAAAAATCCCCCCGAGCGGGGGGATCTCAAAACAATTAGTGGGATTCA +CCAATCGGCAGAACGGTGCGACCAAACTGCTCGTTCAGTACTTCACCCATCGCCAGATAG |