Mercurial > repos > iuc > quast

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+**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/quast.xml	Tue Sep 13 14:43:54 2016 -0400
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+<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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Quast_report.tex	Tue Sep 13 14:43:54 2016 -0400
@@ -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}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Quast_report.tsv	Tue Sep 13 14:43:54 2016 -0400
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Quast_report.txt	Tue Sep 13 14:43:54 2016 -0400
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs_1.fasta	Tue Sep 13 14:43:54 2016 -0400
@@ -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