# HG changeset patch
# User lionelguy
# Date 1378986414 14400
# Node ID d82f18c76309c72a5a37cbc2dc1cbdffc572d225
# Parent  b5ce24f34dd75ddef389fccf8b9dc2671340bd0f
Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.

diff -r b5ce24f34dd7 -r d82f18c76309 tools/spades_2_5/spades.xml
--- a/tools/spades_2_5/spades.xml	Thu Sep 05 07:43:48 2013 -0400
+++ b/tools/spades_2_5/spades.xml	Thu Sep 12 07:46:54 2013 -0400
@@ -1,7 +1,7 @@
-<tool id="spades" name="spades" version="0.5">
+<tool id="spades" name="spades" version="0.6">
   <description>SPAdes genome assembler for regular and single-cell projects</description>
   <requirements>
-    <requirement type="package" version="2.5.0">spades</requirement>
+    <requirement type="package" version="2.5.1">spades</requirement>
   </requirements>
   <command interpreter="perl">spades.pl 
      $out_contigs 
@@ -11,13 +11,15 @@
      $out_log 
     ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output
     spades.py
+    ## Forces unzipped output, faster
+    --disable-gzip-output
     $sc
     $onlyassembler
     $careful
-    $rectangle
+    $rectangles
     -t $threads 
     -k $kmers 
-    -i $iterations 
+    ##-i $iterations 
     ##--phred-offset
     ## Sequence files
     #for $i, $library in enumerate( $libraries )
@@ -30,12 +32,12 @@
       --$prefix$num-$library.orientation    
       #for $file in $library.files
 	#if $file.file_type.type == "separate"
-          --$prefix$num-1 $file.file_type.fwd_reads
-          --$prefix$num-2 $file.file_type.rev_reads
+          --$prefix$num-1 fastq:$file.file_type.fwd_reads
+          --$prefix$num-2 fastq:$file.file_type.rev_reads
         #elif $file.file_type.type == "interleaved"
-          --$prefix$num-12 $file.file_type.interleaved_reads
+          --$prefix$num-12 fastq:$file.file_type.interleaved_reads
         #elif $file.file_type.type == "unpaired"
-          --$prefix$num-s $file.file_type.unpaired_reads
+          --$prefix$num-s fastq:$file.file_type.unpaired_reads
         #end if
       #end for
     #end for
@@ -47,11 +49,11 @@
     </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="rectangle" type="boolean" truevalue="--rectangle" falsevalue="" checked="False" label="Use rectangle correction 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="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="iterations" type="integer" label="Number of iterations for read error correction." value="1"> -->
+    <!-- </param>     -->
     <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 -->
@@ -110,11 +112,22 @@
   <help>
 **What it does**
 
-Runs SPAdes 2.5.0, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage.
+SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.
 
-**Citation**
+This wrapper runs SPAdes 2.5.1, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. 
+
+**SPAdes citation**
 
 Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner. Journal of Computational Biology. May 2012, 19(5): 455-477. doi:10.1089/cmb.2012.0021. 
-    
+  
+**License**
+
+SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
+
+This wrapper is copyrighted by Lionel Guy, and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+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/.
   </help>
 </tool>
diff -r b5ce24f34dd7 -r d82f18c76309 tools/spades_2_5/tool_dependencies.xml
--- a/tools/spades_2_5/tool_dependencies.xml	Thu Sep 05 07:43:48 2013 -0400
+++ b/tools/spades_2_5/tool_dependencies.xml	Thu Sep 12 07:46:54 2013 -0400
@@ -3,7 +3,7 @@
     <package name="spades" version="2.5.0">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.0/SPAdes-2.5.0-Linux.tar.gz</action>
+                <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.1/SPAdes-2.5.1-Linux.tar.gz</action>
                 <!-- Copying the whole bin folder -->
 		<action type="make_directory">$INSTALL_DIR/bin</action>
 		<action type="make_directory">$INSTALL_DIR/share</action>
@@ -16,16 +16,16 @@
 		  <destination_directory>$INSTALL_DIR/share</destination_directory>
 		</action>
 		<!-- This is required to have spades accept .dat files -->
-		<action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
+		<!-- <action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action> -->
+                <!-- <action type="set_environment"> -->
+                <!--     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> -->
+                <!-- </action> -->
             </actions>
         </install>
         <readme>
-This installs SPAdes 2.5.0.
+This installs SPAdes 2.5.1.
 
-See manual here http://spades.bioinf.spbau.ru/release2.5.0/manual.html
+See manual here http://spades.bioinf.spbau.ru/release2.5.1/manual.html
 See also here http://bioinf.spbau.ru/en/spades
         </readme>
     </package>