| Previous changeset 6:1b1af74a54ae (2013-09-12) Next changeset 8:ff058438080a (2014-02-05) |
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Commit message:
Uploaded |
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modified:
tools/spades_2_5/filter_spades_output.xml tools/spades_2_5/spades.pl tools/spades_2_5/spades.xml |
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added:
CHANGE |
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| diff -r 1b1af74a54ae -r 95ddc2380130 CHANGE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CHANGE Thu Nov 28 05:29:32 2013 -0500 |
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| @@ -0,0 +1,17 @@ +0.7 +=== +(thanks to Nicola Soranzo for fixing these bugs) +- spades.pl doesn't die when NODE number is 0 +- removed the --rectangles option (will be deprecated in SPAdes 2.6), because it uses a different seqid format +- switched the --threads parameter to $GALAXY_SLOTS +- a few minor improvements + +0.6 +=== +- Supports SPAdes 2.5.1 +- Disables gzipped output for corrected reads +- Removes the hack that was necessary to accept .dat files (thanks to SPAdes + new input format +- Adds licensing information + +(started at version 0.6) \ No newline at end of file |
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| diff -r 1b1af74a54ae -r 95ddc2380130 tools/spades_2_5/filter_spades_output.xml --- a/tools/spades_2_5/filter_spades_output.xml Thu Sep 12 07:49:07 2013 -0400 +++ b/tools/spades_2_5/filter_spades_output.xml Thu Nov 28 05:29:32 2013 -0500 |
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| @@ -26,8 +26,8 @@ <help> **What it does** -Using the output of SPAdes (a fasta and stats file, either from contigs or scaffolds), it filters the fasta files, discarding all sequences that are under a given length or under a given coverage. +Using the output of SPAdes (a fasta and a stats file, either from contigs or scaffolds), it filters the fasta files, discarding all sequences that are under a given length or under a given coverage. -Typically, this is used to discard short contigs, or contaminations. To dispaly a coverage vs. length plot, use the "SPAdes stats" tool in the same package. +Typically, this is used to discard short contigs, or contaminations. To display a coverage vs. length plot, use the "SPAdes stats" tool in the same package. </help> -</tool> \ No newline at end of file +</tool> |
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| diff -r 1b1af74a54ae -r 95ddc2380130 tools/spades_2_5/spades.pl --- a/tools/spades_2_5/spades.pl Thu Sep 12 07:49:07 2013 -0400 +++ b/tools/spades_2_5/spades.pl Thu Nov 28 05:29:32 2013 -0500 |
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| @@ -76,9 +76,8 @@ while (<FASTA>){ next unless /^>/; chomp; - my @a = split(/\s/, $_); - my ($NODE, $n, $LENGTH, $l, $COV, $cov) = split(/_/, $a[0]); - die "Not all elements found in $_\n" unless ($n && $l && $cov); + die "Not all elements found in $_\n" if (! m/^>NODE_(\d+)_length_(\d+)_cov_(\d+\.*\d*)_/); + my ($n, $l, $cov) = ($1, $2, $3); print TAB "NODE_$n\t$l\t$cov\n"; } close TAB; |
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| diff -r 1b1af74a54ae -r 95ddc2380130 tools/spades_2_5/spades.xml --- a/tools/spades_2_5/spades.xml Thu Sep 12 07:49:07 2013 -0400 +++ b/tools/spades_2_5/spades.xml Thu Nov 28 05:29:32 2013 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="spades" name="spades" version="0.6"> +<tool id="spades" name="spades" version="0.7"> <description>SPAdes genome assembler for regular and single-cell projects</description> <requirements> <requirement type="package" version="2.5.1">spades</requirement> @@ -16,9 +16,9 @@ $sc $onlyassembler $careful - $rectangles - -t $threads - -k $kmers + ##$rectangles + -t \${GALAXY_SLOTS:-16} + -k "$kmers" ##-i $iterations ##--phred-offset ## Sequence files @@ -49,17 +49,14 @@ </param> <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" /> <param name="careful" type="boolean" truevalue="--careful" falsevalue="" checked="True" label="Careful correction?" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." /> - <param name="rectangles" type="boolean" truevalue="--rectangles" falsevalue="" checked="False" label="Use rectangle graph algorithm for repeat resolution?" help="Uses rectangle graph algorithm for repeat resolution stage instead of usual SPAdes repeat resolution module (experimental, use at your own risks)." /> - <param name="threads" type="integer" label="Number of threads to use" value="16"> - </param> - <!-- <param name="iterations" type="integer" label="Number of iterations for read error correction." value="1"> --> - <!-- </param> --> + <!-- <param name="rectangles" type="boolean" truevalue="- -rectangles" falsevalue="" checked="False" label="Use rectangle graph algorithm for repeat resolution?" help="Uses rectangle graph algorithm for repeat resolution stage instead of usual SPAdes repeat resolution module (experimental, use at your own risks)." /> It uses a different format for the sequence identifier in the output FASTA files which do not contain the coverage information --> + <!-- <param name="iterations" type="integer" label="Number of iterations for read error correction." value="1" /> --> <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." > </param> <!-- Reads --> - <repeat name="libraries" title="Libraries"> + <repeat name="libraries" title="Libraries" min="1" help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided."> <param name="lib_type" type="select" label="Library type"> - <option value="paired_end">Paired end / Single reads</option> + <option value="paired_end">Paired-end / Single reads</option> <option value="mate_paired">Mate pairs</option> </param> <param name="orientation" type="select" label="Orientation"> @@ -67,7 +64,7 @@ <option value="rf"><- -> (rf)</option> <option value="ff">-> -> (ff)</option> </param> - <repeat name="files" title="Files"> + <repeat name="files" title="Files" min="1"> <conditional name="file_type"> <param name="type" type="select" label="Select file format"> <option value="separate">Separate input files</option> @@ -97,11 +94,8 @@ </outputs> <!-- <tests> <test> - <param name="sc" value="false" /> <param name="careful" value="false" /> - <param name="rectangle" value="false" /> - <param name="threads" value="16" /> <param name="kmers" value="33,55" /> <param name="type" value="pairedend" /> <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" /> @@ -129,5 +123,11 @@ This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/. + +** Acknowledgments ** + +Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes. + +Nicola Soranzo fixed bugs in the 0.6 version. </help> </tool> |