| Previous changeset 0:d81360ea69d8 (2016-06-28) Next changeset 2:0e2b4e3f9ca1 (2018-08-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit 86047b0de9e8a4d26d756049543f87e94e3ec3ae |
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modified:
velvetoptimiser.xml |
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removed:
test-data/contigs.fa tool_dependencies.xml velvet.xml |
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| diff -r d81360ea69d8 -r 7db5615f4621 test-data/contigs.fa --- a/test-data/contigs.fa Tue Jun 28 17:30:32 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1771 +0,0 @@\n->NODE_1_length_2499_cov_8.185675\n-AAGTGATTTCAGTTCACGCTGCTGGATGTGGTGAGACCTAGTGCGAGTGTTACGGTGCGC\n-TAACCGCGAAGGTCACCGCTCAAGGGGAAACTACCCTGTTTGGGTGAAACTCCTATGGTG\n-GACGCGAACTAACGGAAGAATACATCTCTGTCGCATTAAATAACGTCGCGGCGTCCCCTA\n-TGGGTGCTGCTCCAGTTACAGTCATTCAAAATTGCGATCGACAGCGCAGTAAGGACCGCC\n-GGACAGACCCTCGTTTGCTAAACGGCATTCAGTATAGTCTCACTAATGCGGCGTAACATA\n-CTGCAGCGCGGGGTGGTCACTTGGGGGTGGAACGCCAGAGAGAGCGCATCCTAACTGTGC\n-CGCTCGACAATAGAGTGTAGCCCCCGAACTCTCGGGAGAATTACTGCGGCATGCAATCAA\n-ACTCTCATAATTTTATCCCTGCGCGTCCACCAGCCCGCAGCTCCGGATTCTGGCTAAACA\n-CGATTGAGTAACTGGCAGATTTCCCACCAGGCAGAAAAGAAGCTATAACCAAACCCGGTG\n-ACAATAAACGACCCCCACGCGGCTTGACATAAAAAAACACTATACAGCCAGAGTTCCTTC\n-TTCTTCTTGTCGTAGAAACCATCGGAATATATGCGCTGACCCTCCGCCGTTTGACCCCAC\n-ACAGGGTCAATGCGTTAAATTTGGATTCCTGCAGATATACTTTCGGAGGACGATAATTCA\n-GTCTCCGCCGGAGCCATCGGGAAGTAGGTTGCGAATCGAGCTTTAATAGCGACGGCGATC\n-TGGCGTATCAGGTCCACAATGGTTACAGCATAGCCAACTGGCACGGCAGCTATTATAACG\n-AAGGGAGGCGATTCCGTGGCACGTAGTCGATTCCCTCACTGGGCTTTGGCTGTCCTTAAG\n-CTCGCGCGGGCAAAGTTCCCTCTGGCCGCGAGCCAGTCCGAGGAGAAGGCTCGTTCAATC\n-GTAAAAGTGTCGGAGAAGGGAGTGCGTCTGGCCGCCTACCTGTCGCGTAACAGCGTTGAG\n-ATAGCCTACACCTAGCGAAGCGGTTATGGTCTGCCAGAAACGCAGTCAAGGCAAATCTCT\n-TGGCTTCGAGGCATCGGGTGACTAGATTTCGGTCATACCATTCTGGGACCTCGGGAGCTG\n-GGAGTACTGGACCCCTATTCAGGGCATTGGCAAGGTGTTACTGGATCAGCCGTAAAATAG\n-GCTGTCGGCCGGAACATGCCTGTTGATTTTCCCAAAGGGTTCCTCGTCCAGATGTCGTAC\n-GGTTGTAACGTATCTCTGGATACGGATATAGGGCCAACCCAACTCAACGGCCTGTCTTGG\n-TAACCGCCTGGTTTTATTCCGTTCCGGACATAATCCCTGCCAAATTCGTGACCTGTCATT\n-CGTCGCTTACACGCGCATATCAATTGGATCTAATCGAACAGGCATTCTGCTACTTAGCCC\n-GACGTGATTGTCACCTAGGTACTCCGGTTTACTCATTAGGGGTGTACTTAGTCCAGTGCG\n-CCACGAAGAGATAACTATTTTCGATTTGCACTGCAACAGCGTATTGGTCCTATCAGATAG\n-ACCGGCGTCCCTACGTTCGAGCACTCTTAACACGGATCTAGAAGGGCCTTGGCGTATTTA\n-TCAATTATAATGATAGGCACAGTCATCAGCACGACCTGATGACGTCCCGCTTTGATCGTT\n-TTACAGGTATTGTAAGGCAAGTTCCACTGAGCATGACATCTGTGTTCCCCCTACCCCGAT\n-GTAGGGGTGGAGATATGCATGGTGTAAAGATATTTCCCATTACATGTGTACGGAACAACG\n-CATATGGATGTTTCTGTGAGGGAAGCCTCGCGGATCGCCGTCCGGACCGCTCTACGCTCG\n-CGCATACCCTTAAATGAATTCGACGCTTAAGGGTGCTTTAGGAGTTATTTGCGGGAACAA\n-CGGTCACAAAAGGACCACCTCTATGGTGTTGACCAGCCGCCGATTCCTGGGTCTGTCGCC\n-CACTCCCGGAATGATCCAATGTTTGCTTTAACAGACTCAGCACAAACCAGAGCTGTCCGA\n-CTCGCCTATTGATAATAGACACTCACACGGGACTGGCCTACCAACCAGTATTCGAGAATG\n-GCGACAGGGCGTTGTATTGGACCCACTACTGAACACCGTTACGTAGTTCGGCTTTTCGTG\n-CGGGTGTACTACAGAAATAGCGTCCGAGCACGGTACGACTTCATAAAATAGCGGGTAGGC\n-GTAAGACAATTTATTATTCTTTACCGAGAGTTCTTAACAAAAAATTCTGGGCCGGTAGCA\n-CATGATGAATAATAAGTCCCTTGCCAACTCGACCGCACCAAGATGCCGGTTGGGTAGTCC\n-ATCCCATCCAGCGGACTCTGAGATATTTGAAGAGTCGGGTTAACTAGGCCAGAACATATC\n-AATAGTCACATAATGTTAGAGGGGTTGGTGAAGTAAGGAAGTAGGGGCTACCGATCTCAT\n-TATCTTCGCCGTAGGGCATAACCGCAAACATCAGGTGACTCTTGGCATCATCCATGATGC\n-TGGTACT\n->NODE_2_length_1616_cov_8.225247\n-AAGGGACCTCGGGAGTTACCGCTCTTCGGCTCCCAAATGCTCTGACGCGTCAGTTAATGA\n-TGCAAAGTAACAAGTGGGTCACCCGTGTTTTGCAGATCCTTGACTAGCCCTTGCGGTGAA\n-CGAAAAGAGGGCTTGCGACGGCATGAGGACAACTCACTCATGGCACAACTCGTTCTTACT\n-AAGACCGAATGCCAAATAGGTCCTTACATCATGAGACGGGCCAAATCAAACACACTAATA\n-GTACTTGGAACACAGTGCTAGAGGTATACATCTCGAGCCTGACCCCTGGGCTCCGGTGAT\n-ACGTGAGGGACAGACTGCAGATAGGTCTGGCAGCAACCACGCGGCAGTACCGAAAGCGCC\n-TTAGTGTTTGGTTGAGTACCAACCTCATGCACACGTGAATTAGAGTACAATGCAATGGGC\n-CGGAGCGGCAAGCTTAGACCGTCCCCAACTGATCGTTCCGGCGCATGACGAACTCAAAGA\n-TACTCACATAAAAGGTCTAAAATAGAGTACGTTCCAACAGTCCCAGGCGTAACGCTAAAA\n-CCCGAATGCGACAGGTTTAGCGGGCAGTGGGGACGCGACTGCTAGGGCCCTGACTCCTCT\n-CATGGCTGGAACGACCAACGCGTGTTACCATGCCGATTCACTTATATCTGTGGTCCCTCG\n-GCTCGTGGCCCAAGACCAGATTACGCTGCTGATAGTCAAACGTGATGAAGTGAGCTATTA\n-AGCTGGGCGCAGCTTTGTCGCAAAGGATGAGATTAATAAATAGCATGACACACCAGTTCC\n-AGAGTTTGAACCTGTACCGAGTATGAACGGCCGAGAGTAGATGGACCAGGATCTGAGGTA\n-TAGCGTTTGCACGAATTTAGAAAAATACGTCCCTCGAGGAGTATACGAGTCATATGACAC\n-CCTGGTTATGTGGTAAGTGCTAAATCGTTGCGTTGCTAAATTGGAACATCAGAGGACTCC\n-GCTCACAGAAGCTCATAATCACTAAGGAATCCCCACATTTCAATATTTTCCTACCACTGT\n-CAATAACCGGGCAAAATCCTATGATCCCCCGGTACGCGGAGCATAGGTACCATAGCATTG\n-CCAAGGTAACTGACAAGAGTCACCTGGCCCCATGACCGACACGTTTGGGCCTATTGAATA\n-CTTCAGAACGGCGGAAAAAGAGAGGGGTGTATGCCTACCTATACGTACACGCTCTTTGGG\n-ATGGATGAACTGCAAATGGGGAGTGAAACGACGGATGACCTGCAAGCATGTGCCGCGC'..b'GGCTGTAGCCCCGAACGT\n-GCAAAACTAGCTGGTCTTGGATGAAACAGAGCCTGAAGCATTTCGTGAGGTTGCGAGACA\n-TGGATTGTGGCGATGGAAAGTCAGTCGCCGCGTGGTATCACCTCGCCCAGCAGGTCAAAG\n-GGTTCGCACTATTCTAATTTTGCAGGACCCGTACCCACTCAGTGAAAATAGGAGTACGGC\n-CCCGATCGCCCCCTGTATGAATGTAAGTCATGAGCGCTATTGGCGGCAGGCAGCACTCTG\n-ACACACCCTCAGTTTCTGGCTTTCGTCAACCGATTGCTACCAGCTAGCTTCCAATCGTGG\n-AGGGCTCTCTGTACGCCTTCGCGGCTTTGTTGAGACCCACGCAGTTCTAGGTTGTCATTA\n-TCCGATATGTATCCATGTACGTTCGT\n->NODE_46_length_647_cov_7.907264\n-ACCCGCACTAAGCCGTAGGCGCGACAACTAGTTTAACTAAGTTGAAAGTCGCTCTTCTGT\n-CGGGGAAACAATGTCCAGTCCAGTATACGACGTCCCTTTCCCCCGGCGCGTCAGGGAATT\n-ATACCGGCCCTAGGTACGGTGAGCCGGCTTGGCGTTAAGATAACCCCCTGCAGTGAGGGC\n-CTGCCGCTACACGGATCGTGTCGCCTCAAGGTGTACCTTTGCAGCCTGGGACTGAAGGGA\n-AGTACACGACGTTTGGGCCAGCCTACCCCTCTAGGTATTACGAAACACGATGATCGTCTG\n-TGAACGTTCATACTTTGACTTTCCTTGCGACGACCCAGAAGTAGATCGACGCACGCACTT\n-TAAGAGCTTATAGCAGGTTTCAGGAAGACGGATCCATATGCGTAGCGGCTAGTCTTGTCA\n-GATTGAAATCTATCCTTGCGTTGTGACCAACTGGGCAGAGCCGTGGCAGGTAAGCATAAA\n-GGAACTAGATTGGTCCTTAGCCGAGATGGCACAATTGCGGATAATCCCCGTAGGATCCGA\n-CTGACCAAATCTTGTGTGCATAATAGACAGCAGAAAAAGCTGTAGAAGGAAAACGGCGTT\n-TCTCTTCTAACGTGATGTGCAGCCTTTCGCTGCATTGCCCAGGTAACAGTTGGCCCCCCT\n-TTGCCCCAATTCCCC\n->NODE_47_length_407_cov_8.117936\n-AAGAAAAGCAGGGTTATACAATAGAGAGCGCCTTCTTCCCCTTAGGACGGGTCGCCAGTC\n-AAGTTAGGCTTTGGTACTGTCAGGGATTGGAGGTGCTAAAATTGGGTTGCGTCCGTCCGT\n-ATCGGTACAACATCGCTCACGTCTATTCACAAACTGCTTCTCCGGTACCATTTATTTGAT\n-TAAAGTGTGGACTCTCATGCACCTCATAGTACAACGTACCGCGCGCGGCAACGCATCTAT\n-TAATAGCTGGAATGCCTTTATTCCAGCCCCAACCTCTAACGACCGGGCCGGACTGGCTTT\n-AATCCTGATGCGGGTAAGCCATCCTTTAGTTGTTTAGCACTCTCTTCTCTACGCGCCGGT\n-CCGAACAGTAAGCTAAGCTTATATATACCGCGATGAAGTTGTGTGGTCTGAACCTCATTC\n-GATGTCGTTCTCACA\n->NODE_48_length_215_cov_7.604651\n-CGGCAGAGCCCCGACGGGATCTGGAGTCACACAGGTCTCGATTGTAACTAAATGGTCGCC\n-TCGTAAGCTATATGGGTTTGTTGTGAGTGTAGCGCCGAGGACGTTACGTAATTGGCTAAC\n-AATCGCGCCATCCCAACCTCCTAAGGGCGGGGTGTCTCGACCCGGCTAGGCTCCTTTCAC\n-ATATCTAACTAGACCTGATAGATTCGTAATCAGCTTCTTGGTATACGGCCGTCCTGAGGA\n-CTA\n->NODE_49_length_184_cov_7.711957\n-CAGACTGGTTCCTTTGGTATCGGCTGACTGCGGGTTTTACTGCAATCGGGCTGTCCGCTA\n-TGTGGTGGTCTGCCTGCGAGTCCAATCGCAAATTTAAAGAACTGAACGGTATAGGGCACA\n-ACATGGCTACACAGCCCCCTGGACACAATTTCGCCGGTGGACTGCTACGGGACTAACAAG\n-CCTTTCTTTAGCAAGTACTCCGTACTTGTGGC\n->NODE_50_length_328_cov_8.512196\n-CCCGAAGTCGACAGTGAATAGCGCGCGCTTTACATCACAGTATTGTGGTCTGTCTCGCGC\n-CCGGCCTGGTACTTACGGTGAGATATAGATACAGTGTGACCAGATGCGCCACTAATTAGT\n-TGCAAAGTTGAAGGCCAGTCTTGTTGGGTAGGGTGGTACGGCTATAGAGCCGCACAGTTC\n-ACAGAGCTTGGCACGTCATTCCCGCGTTGGCGTCATTCGGAAAACGTGGTGTATGCGCAA\n-TCGGGGCGATAAAAACGTAAGGAGCGTTTATGCCAAACGAAGAATAGCTGGGAGACAACT\n-AACCGCCGGTGGGGTCGCGCTATTGAAGACCAGGCATTGCGAAAGTCAAACTACGT\n->NODE_51_length_716_cov_7.587989\n-ACCAGGCATTGCGAAAGTCAAACTACGTCGCCATCGCGGCCAGAAGAGCGGCGTAGAGCC\n-CTGCGTTTGCATCTTCCATTGCAAACGCTAGATCCCAAAGCCGGACTCCGATTCTAGGCC\n-GTGCATGCAGTCTCATTTCAGCACGTCACGGTGAAGTGTTCTCAACATACAGGAACTCCC\n-ATAGTCATTAGATTCTACTCGTTATTCGCTTCGATGCTCATTCGTGGTTCACAACTTTCA\n-GCCACAGGATGTTTGGCACACGCCGTACGCGAGTATATCAGATCTCTCCCCGTTTCGTGA\n-CAATAATATAAGATTACTCGAGCTCAATAGTCTTATATTTATCAGCATACGAATTCTTCT\n-CAAAACTAAGTACCCAGCTGTCGTACAAACTCGAGGCCGCACGCGTCAACGTGAGTCTTC\n-AGTGGCATGGCGATAGGCTGGCGCGAATTTCACAGACTTTCAGCTGACTTAGAGTGGTGG\n-GTGTTATATTTCTCGTTGATCACGGAACTGTCCCAACAACTAGGCACCTGAAGCGCCTGA\n-CCCTGCTTCAAAAGTCTAGGGGGCTCGAAAACCCATTAGAATCACACAAAGTGCAGGGGG\n-GTTTAAGTAAAATCACCCCCCAAACAGTGACATATAACTAGTACAAGCGATTATTCACAG\n-GCTCCGCGACGGATTCTGGCGCCGCATCGTTAAGCCCTTCAGTACGCAAAGGCTAGTTTC\n-GTCGCTAGGTTGCGGGCATCACAC\n->NODE_52_length_131_cov_7.816794\n-ACAATAAGTTAAAGGAGCCAGAGAGATAGCGGTGTGGTACGACGGTGCAACGATGGTCGC\n-TATGGGAACAGTCTGTTAATACGAAAGTGAACAATGGTTATCTAACATGATGGCTGCCGT\n-GGAGGTCCGACGCAGCGGCATAGCCCTGTCGCAGTGGAT\n->NODE_53_length_219_cov_7.424657\n-GTGATGATTCATTGCTCTGCTACTTCCGAATTTCTGATCTACGAAATCTCGGGTCCCTTC\n-TGAGATAAGCTTGGTGGGACTGACGCTTAGATCCCCACCTGAGCGCTATTGGGGAATTTA\n-CTTGACTCGAACCGGTTCAGCGATAATTTGTCCTTGATTGTTTACCAATAGAGGTGTGCG\n-ACTCATTAGGGCCGGGTGGGGAGATCGGTTATAACATAACTTGACATAGCTAGCACTGTG\n-GTGGTTT\n->NODE_54_length_60_cov_6.783333\n-ACCCGATGCCTGGCACGTTCCTGGGAACAGCCTGGGGCATGAGACGGACCCGATATACAA\n-TCCTAACGCCGACAATGGTATAGATTTT\n' 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| diff -r d81360ea69d8 -r 7db5615f4621 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jun 28 17:30:32 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,21 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="velvet" version="1.2.10"> - <repository changeset_revision="a6d81014257d" name="package_velvet_1_2_10" owner="simon-gladman" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="velvetoptimiser" version="2.2.5"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://www.vicbioinformatics.com/VelvetOptimiser-2.2.5.tar.gz</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> - <action type="shell_command">chmod ugo+x $INSTALL_DIR/bin/VelvetOptimiser.pl</action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - </package> -</tool_dependency> |
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| diff -r d81360ea69d8 -r 7db5615f4621 velvet.xml --- a/velvet.xml Tue Jun 28 17:30:32 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,120 +0,0 @@ -<tool id="velvet" name="velvet" version="0.1.0"> - <requirements> - <requirement type="package" version="1.2.10">velvet</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - - <command><![CDATA[ - velveth - out - $kmer - #for $i in $files: - -${i.filetype} - - #if str($i.paired_type.paired_type_selector) == "paired": - - #if $i.__index__ > 1: - -shortPaired$i.__index__ - #else - -shortPaired - #end if - - -separate $i.paired_type.input1 $i.paired_type.input2 - #end if - - #if str($i.paired_type.paired_type_selector) == "single" - - #if $i.__index__ > 1 - -short$i.__index__ - #else - -short - #end if - - $i.paired_type.input1 - #end if - - #if str($i.paired_type.paired_type_selector) == "paired_collection" - #if $i.__index__ > 1 - -shortPaired$i.__index__ - #else - -shortPaired - #end if - -separate $i.paired_type.input1.forward $i.paired_type.input1.reverse - #end if - #if str($i.paired_type.paired_type_selector) == "paired_iv" - #if $i.__index__ > 1 - -shortPaired$i.__index__ - #else - -shortPaired - #end if - $i.paired_type.input1 - #end if - #end for - - && - - velvetg out > $log - ]]></command> - <inputs> - <param name="kmer" type="integer" value="29" label="K-mer" help="The kmer value to use for velvet - must be an odd integer between 19 and 191" /> - <repeat name="files" title="Input files" min="1"> - <param name="filetype" label="Input file type" type="select" help="Input file type"> - <option value="fastq">Fastq</option> - <option value="fasta">Fasta</option> - <option value="bam">Bam</option> - </param> - <conditional name="paired_type"> - <param name="paired_type_selector" type="select" label="Single or paired end reads" help="Select between paired and single end data"> - <option value="paired">Paired</option> - <option value="single">Single</option> - <option value="paired_collection">Paired Collection</option> - <option value="paired_iv">Paired Interleaved</option> - </param> - <when value="paired"> - <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select first set of reads" help="Specify dataset with forward reads"/> - <param name="input2" type="data" format="fastqsanger,fasta,bam" label="Select second set of reads" help="Specify dataset with reverse reads"/> - </when> - <when value="single"> - <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select the reads" help="Specify dataset with the reads"/> - </when> - <when value="paired_collection"> - <param name="input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> - </when> - <when value="paired_iv"> - <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select set of interleaved reads" help="Specify dataset with interleaved paired reads"/> - </when> - </conditional> - </repeat> - - </inputs> - <outputs> - <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/> - <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Contig Stats" from_work_dir="out/stats.txt"/> - <data format="tabular" name="graph" label="${tool.name} on ${on_string}: Last Graph" from_work_dir="out/LastGraph"/> - <data format="tabular" name="log" label="${tool.name} on ${on_string}: log" /> - </outputs> - <tests> - <test> - <param name="kmer" value="29" /> - <param name="files_0|filetype" value="fasta" /> - <param name="files_0|paired_type|paired_type_selector" value="single" /> - <param name="files_0|paired_type|input1" value="test_reads.fa" ftype="fasta" /> - <output name="contigs" ftype="fasta" file="contigs.fa" /> - </test> - </tests> - <help><![CDATA[ - The Velvet wrapper, wraps both velveth and velvetg for single kmer value with no parameters supplied to velvetg. It is mainly for teaching how kmer size affects the assembly. - - It returns the contigs.fa file, the contig_stats.txt file, the LastGraph file and captures the screen output to the log. - - This tool is mainly wrapped for assembly teaching purposes. It should not be used for actual assemblies. Please use the Velvet Optimiser for this purpose. - - The kmer value supplied needs to be an odd integer. - ]]></help> - <citations> - <citation type="doi">10.1101/gr.074492.107</citation> - <citation type="doi">10.1371/journal.pone.0008407</citation> - </citations> -</tool> \ No newline at end of file |
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| diff -r d81360ea69d8 -r 7db5615f4621 velvetoptimiser.xml --- a/velvetoptimiser.xml Tue Jun 28 17:30:32 2016 -0400 +++ b/velvetoptimiser.xml Thu Dec 21 18:23:10 2017 -0500 |
| [ |
| b'@@ -1,150 +1,138 @@\n-<tool id="velvetoptimiser" name="VelvetOptimiser" version="1.1.0">\n+<tool id="velvetoptimiser" name="VelvetOptimiser" version="2.2.5">\n+ <description>Automatically optimize Velvet assemblies</description>\n <requirements>\n- <requirement type="package" version="1.2.10">velvet</requirement>\n- <requirement type="package" version="2.2.5">velvetoptimiser</requirement>\n+ <requirement type="package" version="1.2.10">velvet</requirement>\n+ <requirement type="package" version="2.2.5">perl-velvetoptimiser</requirement>\n </requirements>\n- <stdio>\n- <exit_code range="1:" />\n- </stdio>\n+ <version_command>VelvetOptimiser.pl --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ export OMP_NUM_THREADS=2 &&\n+ export OMP_THREAD_LIMIT=2 &&\n+ VelvetOptimiser.pl\n+ -t "\\${GALAXY_SLOTS:-1}"\n+ -s $start_kmer\n+ -e $end_kmer\n+ -d out\n+ -f "\n+ #for $i in $files:\n+ -${i.filetype}\n \n- <command><![CDATA[\n- export OMP_NUM_THREADS=2 &&\n- VelvetOptimiser.pl\n- -t \\${GALAXY_SLOTS:-2}\n- -s $start_kmer\n- -e $end_kmer\n- -d out\n- -f "\n- #for $i in $files:\n- -${i.filetype}\n+ #if str($i.paired_type.paired_type_selector) == "paired":\n \n- #if str($i.paired_type.paired_type_selector) == "paired":\n+ #if $i.__index__ > 1:\n+ -shortPaired$i.__index__\n+ #else\n+ -shortPaired\n+ #end if\n \n- #if $i.__index__ > 1:\n- -shortPaired$i.__index__\n- #else\n- -shortPaired\n- #end if\n+ -separate \'$i.paired_type.input1\' \'$i.paired_type.input2\'\n+ #end if\n \n- -separate $i.paired_type.input1 $i.paired_type.input2\n- #end if\n-\n- #if str($i.paired_type.paired_type_selector) == "single"\n+ #if str($i.paired_type.paired_type_selector) == "single"\n \n- #if $i.__index__ > 1\n- -short$i.__index__\n- #else\n- -short\n- #end if\n+ #if $i.__index__ > 1\n+ -short$i.__index__\n+ #else\n+ -short\n+ #end if\n \n- $i.paired_type.input1\n- #end if\n+ \'$i.paired_type.input1\'\n+ #end if\n \n- #if str($i.paired_type.paired_type_selector) == "paired_collection"\n- #if $i.__index__ > 1\n- -shortPaired$i.__index__\n- #else\n- -shortPaired\n- #end if\n- -separate $i.paired_type.input1.forward $i.paired_type.input1.reverse\n- #end if\n- #if str($i.paired_type.paired_type_selector) == "paired_iv"\n- #if $i.__index__ > 1\n- -shortPaired$i.__index__\n- #else\n- -shortPaired\n- #end if\n- $i.paired_type.input1\n- #end if\n- #end for\n- "\n+ #if str($i.paired_type.paired_type_selector) == "paired_collection"\n+ #if $i.__index__ > 1\n+ -shortPaired$i.__index__\n+ #else\n+ -shortPaired\n+ #end if\n+ -separate \'$i.paired_type.input1.forward\' \'$i.paired_type.input1.reverse\'\n+ #end if\n+ #if str($i.paired_type.paired_type_selector) == "paired_iv"\n+ #if $i.__index__ > 1\n+ -shortPaired$i.__index__\n+ #else\n+ -shortPaired\n+ #end if\n+ \'$i.paired_type.input1\'\n+ #end if\n+ #end for\n+ "\n \n- #if str($advanced.advanced_select) == "advanc'..b'nly.)\n+\n+ Defaults are:\n \n- \'n50*Lcon\' = The n50 times the number of long contigs.\n+ *n50* for k-mer length optimisation &\n \n- \'n50*Lcon/tbp+log(Lbp)\' = The n50 times the number of long contigs divided by the total bases in all contigs plus the log of the number of bases in long contigs (as an example only.)\n+ *Lbp* for coverage cutoff\n \n **Hash Length**\n \n The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed.\n \n The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints::\n+ - it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.\n+ - it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits\n+ - it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.\n \n- # it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.\n- # it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits\n- # it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.\n-\n- Now you still have quite a lot of possibilities. As is often the case, it\'s a trade- off between specificity and sensitivity. Longer kmers bring you more specificity (i.e. less spurious overlaps) but lowers coverage (cf. below). . . so there\'s a sweet spot to be found with time and experience.\n- We like to think in terms of "k-mer coverage", i.e. how many times has a k-mer been seen among the reads. The relation between k-mer coverage Ck and standard (nucleotide-wise) coverage C is Ck = C # (L - k + 1)/L where k is your hash length, and L you read length.\n+ Now you still have quite a lot of possibilities. As is often the case, it\'s a trade-off between specificity and sensitivity. Longer kmers bring you more specificity (i.e. less spurious overlaps) but lowers coverage (cf. below)... so there\'s a sweet spot to be found with time and experience.\n+ We like to think in terms of "k-mer coverage", i.e. how many times has a k-mer been seen among the reads. The relation between k-mer coverage Ck and standard (nucleotide-wise) coverage C is Ck = C * (L - k + 1)/L where k is your hash length, and L you read length.\n Experience shows that this kmer coverage should be above 10 to start getting decent results. If Ck is above 20, you might be "wasting" coverage. Experience also shows that empirical tests with different values for k are not that costly to run! VelvetOptimiser automates these tests for you.\n \n \n@@ -260,7 +249,7 @@\n \n -max_branch_length integer : maximum length in base pair of bubble (default: 100)\n \n- max_divergence floating-point : maximum divergence rate between two branches in a bubble (default: 0.2)\n+ -max_divergence floating-point : maximum divergence rate between two branches in a bubble (default: 0.2)\n \n -max_gap_count integer : maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)\n \n@@ -300,10 +289,10 @@\n ]]></help>\n <citations>\n <citation type="bibtex">@UNPUBLISHED{GLADMAN2012,\n- author = "Gladman Simon",\n- title = "VelvetOptimiser",\n- year = "2012",\n- note = "https://github.com/slugger70/VelvetOptimiser"}\n+ author = "Gladman Simon",\n+ title = "VelvetOptimiser",\n+ year = "2012",\n+ note = "https://github.com/slugger70/VelvetOptimiser"}\n </citation>\n <citation type="doi">10.1101/gr.074492.107</citation>\n <citation type="doi">10.1371/journal.pone.0008407</citation>\n' |