# HG changeset patch
# User lionelguy
# Date 1385634572 18000
# Node ID 95ddc23801300f7570b20fde242876993b77c361
# Parent  1b1af74a54ae0af6a593081440acda683609df2a
Uploaded

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
@@ -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
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
@@ -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>
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
@@ -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;
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
@@ -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">&lt;- -> (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>