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changeset 0:f74009e6e1e1 draft default tip

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author aafc-mbb
date Wed, 23 Mar 2016 09:41:56 -0400
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files quast.xml test-data/input_contigs_1.fasta test-data/output_Quast_report.txt tool_dependencies.xml
diffstat 4 files changed, 232 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/quast.xml	Wed Mar 23 09:41:56 2016 -0400
@@ -0,0 +1,103 @@
+<tool id="quast" name="Quast" version="1.0.0" >
+	<description>QUAST (Quality ASsessment Tool) evaluates genome assemblies.</description>
+		
+	<requirements>
+		<requirement type="package" version="3.2">quast</requirement>
+	</requirements>
+
+	<stdio>
+	    <exit_code range="1:" level="fatal" description="The tool's exit code was 1, which suggests that something went wrong." />
+	</stdio>
+
+	<command>		
+		quast.py 
+		 -o outputdir
+		
+		#if $gene_selection == "eukaryote" :
+			--eukaryote
+		#end if
+		
+		#if $gene_selection == "Metagenes" :
+			--meta
+                #end if
+		
+		--min-contig $min_contig
+		
+		
+		#for $i in $files:
+			$i.input
+		#end for
+		;
+		cp outputdir/report.txt $quast_out;
+	</command>
+	
+	<inputs>
+		<repeat name="files" title="Input contig files">	
+			<param type="data" format="fasta" name="input" label="Contigs output file"/>	
+		</repeat>
+		<param name="gene_selection" type="select">
+			<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="Set the threshold for the contig length (default is 500)"/>
+	</inputs>
+	
+	<outputs>
+		<data format="txt" name="quast_out" label="Quast report.txt" from_work_dir="Quast_report.txt"/>
+	</outputs>
+
+	<tests>
+		<test>
+			<param name="input" value="input_contigs_1.fasta"/>
+			<param name="gene_selection" value="eukaryote"/>
+			<param name="min_config" value="500"/>
+			<output name="quast_out" file="output_Quast_report.txt"/>
+		</test>
+	</tests>
+	
+	<help>
+**Description**
+		
+Galaxy tool wrapper for the QUAST tool. Quast stands for QUality ASsessment Tool. It evalutes genome assemblies by computing various metrics. 
+For more information regarding the settings of the tool, please visit the QUAST 3.2 Manual on http://quast.bioinf.spbau.ru/manual.html
+
+-----
+
+**Inputs and Outputs**
+		
+- Input:
+	+ The tool accepts assemblies and references in FASTA format. 
+
+- Output:
+	+ An assessment summary in plain text format
+
+
+-----
+
+**Tool Information**
+
+- QUAST Tool v3.2: 
+	+ Release Date: November 2015
+	+ URL: http://bioinf.spbau.ru/quast
+	+ Source URL: https://downloads.sourceforge.net/project/quast/quast-3.2.tar.gz
+
+-----
+		
+**QUAST Galaxy Wrapper Author and Contact Information**
+
++ Jacob Jablonski
++ AAFC-MBB Team
++ Email: mbb@agr.gc.ca
++ Agriculture and Agri-foods Canada, Ottawa, ON, Canada
+
+	</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>
+	</citations>  
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_contigs_1.fasta	Wed Mar 23 09:41:56 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_Quast_report.txt	Wed Mar 23 09:41:56 2016 -0400
@@ -0,0 +1,24 @@
+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                    dataset_1.dat
+# contigs (>= 0 bp)         3            
+# contigs (>= 1000 bp)      3            
+# contigs (>= 5000 bp)      0            
+# contigs (>= 10000 bp)     0            
+# contigs (>= 25000 bp)     0            
+# contigs (>= 50000 bp)     0            
+Total length (>= 0 bp)      6710         
+Total length (>= 1000 bp)   6710         
+Total length (>= 5000 bp)   0            
+Total length (>= 10000 bp)  0            
+Total length (>= 25000 bp)  0            
+Total length (>= 50000 bp)  0            
+# 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/tool_dependencies.xml	Wed Mar 23 09:41:56 2016 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="quast" version="3.2">
+		<repository changeset_revision="0bcf4378cb31" name="package_quast_3_2" owner="aafc-mbb" toolshed="https://toolshed.g2.bx.psu.edu/" />
+	</package>
+</tool_dependency>