# HG changeset patch
# User Takadonet <philipmabon@gmail.com>
# Date 1375467446 18000
# Node ID 095f988dd814dccc84d6fbec336c0ffe40601d41
# Parent  334ed4f2a504b2178670927548ad35e2fa35fc53
Updated to use latest spade release (2.5.0). Cannot fully test since spades server is none responsive

diff -r 334ed4f2a504 -r 095f988dd814 tools/spades_2_4/spades.pl
--- a/tools/spades_2_4/spades.pl	Wed Jul 17 03:45:54 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-#!/usr/bin/env perl
-## A wrapper script to call spades.py and collect its output
-use strict;
-use warnings;
-use File::Temp qw/ tempfile tempdir /;
-use File::Copy;
-
-# Parse arguments
-my ($out_contigs_file, $out_scaffolds_file, $out_log_file, @sysargs) = @ARGV;
-
-# Create temporary folder to store files, delete after use
-#my $output_dir = tempdir( CLEANUP => 0 );
-my $output_dir = tempdir( CLEANUP => 1 );
-# Link "dat" files as fastq, otherwise spades complains about file format
-
-# Create log handle
-open my $log, '>', $out_log_file or die "Cannot write to $out_log_file: $?\n";
-
-# Run program
-# To do: record time
-&runSpades(@sysargs);
-&collectOutput();
-print $log "Done\n";
-close $log;
-exit 0;
-
-# Run spades
-sub runSpades {
-    my $cmd = join(" ", @_) . " -o $output_dir";
-    my $return_code = system($cmd);
-    if ($return_code) {
-	print $log "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
-	die "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
-    }
-    return 0;
-}
-# Collect output
-sub collectOutput{
-    # To do: check that the files are there
-    # Collects output
-    move "$output_dir/contigs.fasta", $out_contigs_file;
-    move "$output_dir/scaffolds.fasta", $out_scaffolds_file;
-    open LOG, '<', "$output_dir/spades.log" 
-	or die "Cannot open log file $output_dir/spades.log: $?";
-    print $log $_ while (<LOG>);
-    return 0;
-}
diff -r 334ed4f2a504 -r 095f988dd814 tools/spades_2_4/spades.xml
--- a/tools/spades_2_4/spades.xml	Wed Jul 17 03:45:54 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,104 +0,0 @@
-<tool id="spades" name="spades" version="0.2">
-  <description>SPAdes genome assembler for regular and single-cell projects</description>
-  <requirements>
-    <requirement type="package" version="2.4.0">spades</requirement>
-  </requirements>
-  <command interpreter="perl">spades.pl $out_contigs $out_scaffolds $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
-    ## TODO: kmers, threads, other options (-sc for single-cell)
-    #if $sc == "true":
-      --sc 
-    #end if
-    #if $careful == "true":
-      --careful 
-    #end if
-    #if $rectangle == "true" 
-      --rectangle 
-    #end if 
-    -t $threads 
-    -k $kmers 
-    -i $iterations 
-    ##--phred-offset
-    ## Sequence files
-    #for $i, $s in enumerate( $reads )
-      #if $s.read_type.type == "pairedend"
-      -1 $s.read_type.fwd_reads
-      -2 $s.read_type.rev_reads
-      #elif $s.read_type.type == "interleaved"
-      --12 $s.read_type.interleaved_reads
-      #elif $s.read_type.type == "unpaired"
-      -s $s.read_type.unpaired_reads
-      #end if
-    #end for
-  </command>
-  <inputs>
-    <param name="sc" type="select" label="Single-cell?" help="This flag is required for MDA (single-cell) data.">
-      <option value="false">No</option>
-      <option value="true">Yes</option>
-    </param>
-    <param name="careful" type="select" 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).">
-      <option value="false">No</option>
-      <option value="true" selected="true">Yes</option>
-    </param>
-    <param name="rectangle" type="select" label="Use rectangle correction for repeat resolution?" help="Uses rectangle graph algorithm for repeat resolution stage instead of usual SPAdes repeat resolution module (experimental).">
-      <option value="false" selected="true">No</option>
-      <option value="true">Yes</option>
-    </param>
-    <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="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 and listed in ascending order). The default value is 21,33,55." >
-    </param>
-    <!-- Reads -->
-    <repeat name="reads" title="Reads">
-      <conditional name="read_type">
-	<param name="type" type="select" label="Select type of reads">
-	  <option value="pairedend">Paired-end, separate inputs</option>
-	  <option value="interleaved">Paired-end, interleaved</option>
-	  <option value="unpaired">Unpaired reads</option>
-	</param>
-	<when value="pairedend">
-	  <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" />
-	  <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" />
-	</when>
-	<when value="interleaved">
-	  <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" />
-	</when>
-	<when value="unpaired">
-	  <param name="unpaired_reads" type="data" format="fastq" label="Unpaired reads" help="FASTQ format" />
-	</when>
-      </conditional>
-    </repeat>
-  </inputs>
-  <outputs>
-    <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" />
-    <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" />
-    <data name="out_log" format="txt" label="SPAdes log" />
-  </outputs>
-  <tests>
-    <test>
-      <!-- Based on the tests coming along with SPAdes -->
-      <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" />
-      <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
-      <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
-    </test>
-  </tests>
-  <help>
-**What it does**
-
-Runs SPAdes 2.4.0, collects the output, and throws away all the temporary files.
-
-**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. 
-    
-  </help>
-</tool>
diff -r 334ed4f2a504 -r 095f988dd814 tools/spades_2_4/tool_dependencies.xml
--- a/tools/spades_2_4/tool_dependencies.xml	Wed Jul 17 03:45:54 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="spades" version="2.4.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.4.0/SPAdes-2.4.0-Linux.tar.gz</action>
-                <!-- Copying the whole bin folder -->
-		<action type="make_directory">$INSTALL_DIR/bin</action>
-		<action type="make_directory">$INSTALL_DIR/share</action>
-		<action type="move_directory_files">
-		  <source_directory>bin</source_directory>
-		  <destination_directory>$INSTALL_DIR/bin</destination_directory>
-		</action>
-                <action type="move_directory_files">
-		  <source_directory>share</source_directory>
-		  <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'/" $INSTALL_DIR/bin/spades.py</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-This installs SPAdes 2.4.0.
-
-See manual here http://spades.bioinf.spbau.ru/release2.4.0/manual.html
-See also here http://bioinf.spbau.ru/en/spades
-        </readme>
-    </package>
-</tool_dependency>
-
diff -r 334ed4f2a504 -r 095f988dd814 tools/spades_2_5/spades.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/spades_2_5/spades.pl	Fri Aug 02 13:17:26 2013 -0500
@@ -0,0 +1,47 @@
+#!/usr/bin/env perl
+## A wrapper script to call spades.py and collect its output
+use strict;
+use warnings;
+use File::Temp qw/ tempfile tempdir /;
+use File::Copy;
+
+# Parse arguments
+my ($out_contigs_file, $out_scaffolds_file, $out_log_file, @sysargs) = @ARGV;
+
+# Create temporary folder to store files, delete after use
+#my $output_dir = tempdir( CLEANUP => 0 );
+my $output_dir = tempdir( CLEANUP => 1 );
+# Link "dat" files as fastq, otherwise spades complains about file format
+
+# Create log handle
+open my $log, '>', $out_log_file or die "Cannot write to $out_log_file: $?\n";
+
+# Run program
+# To do: record time
+&runSpades(@sysargs);
+&collectOutput();
+print $log "Done\n";
+close $log;
+exit 0;
+
+# Run spades
+sub runSpades {
+    my $cmd = join(" ", @_) . " -o $output_dir";
+    my $return_code = system($cmd);
+    if ($return_code) {
+	print $log "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
+	die "Failed with code $return_code\nCommand $cmd\nMessage: $?\n";
+    }
+    return 0;
+}
+# Collect output
+sub collectOutput{
+    # To do: check that the files are there
+    # Collects output
+    move "$output_dir/contigs.fasta", $out_contigs_file;
+    move "$output_dir/scaffolds.fasta", $out_scaffolds_file;
+    open LOG, '<', "$output_dir/spades.log" 
+	or die "Cannot open log file $output_dir/spades.log: $?";
+    print $log $_ while (<LOG>);
+    return 0;
+}
diff -r 334ed4f2a504 -r 095f988dd814 tools/spades_2_5/spades.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/spades_2_5/spades.xml	Fri Aug 02 13:17:26 2013 -0500
@@ -0,0 +1,104 @@
+<tool id="spades" name="spades" version="0.3">
+  <description>SPAdes genome assembler for regular and single-cell projects</description>
+  <requirements>
+    <requirement type="package" version="2.5.0">spades</requirement>
+  </requirements>
+  <command interpreter="perl">spades.pl $out_contigs $out_scaffolds $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
+    ## TODO: kmers, threads, other options (-sc for single-cell)
+    #if $sc == "true":
+      --sc 
+    #end if
+    #if $careful == "true":
+      --careful 
+    #end if
+    #if $rectangle == "true" 
+      --rectangle 
+    #end if 
+    -t $threads 
+    -k $kmers 
+    -i $iterations 
+    ##--phred-offset
+    ## Sequence files
+    #for $i, $s in enumerate( $reads )
+      #if $s.read_type.type == "pairedend"
+      -1 $s.read_type.fwd_reads
+      -2 $s.read_type.rev_reads
+      #elif $s.read_type.type == "interleaved"
+      --12 $s.read_type.interleaved_reads
+      #elif $s.read_type.type == "unpaired"
+      -s $s.read_type.unpaired_reads
+      #end if
+    #end for
+  </command>
+  <inputs>
+    <param name="sc" type="select" label="Single-cell?" help="This flag is required for MDA (single-cell) data.">
+      <option value="false">No</option>
+      <option value="true">Yes</option>
+    </param>
+    <param name="careful" type="select" 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).">
+      <option value="false">No</option>
+      <option value="true" selected="true">Yes</option>
+    </param>
+    <param name="rectangle" type="select" label="Use rectangle correction for repeat resolution?" help="Uses rectangle graph algorithm for repeat resolution stage instead of usual SPAdes repeat resolution module (experimental).">
+      <option value="false" selected="true">No</option>
+      <option value="true">Yes</option>
+    </param>
+    <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="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 and listed in ascending order). The default value is 21,33,55." >
+    </param>
+    <!-- Reads -->
+    <repeat name="reads" title="Reads">
+      <conditional name="read_type">
+	<param name="type" type="select" label="Select type of reads">
+	  <option value="pairedend">Paired-end, separate inputs</option>
+	  <option value="interleaved">Paired-end, interleaved</option>
+	  <option value="unpaired">Unpaired reads</option>
+	</param>
+	<when value="pairedend">
+	  <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" />
+	  <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" />
+	</when>
+	<when value="interleaved">
+	  <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" />
+	</when>
+	<when value="unpaired">
+	  <param name="unpaired_reads" type="data" format="fastq" label="Unpaired reads" help="FASTQ format" />
+	</when>
+      </conditional>
+    </repeat>
+  </inputs>
+  <outputs>
+    <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" />
+    <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" />
+    <data name="out_log" format="txt" label="SPAdes log" />
+  </outputs>
+  <tests>
+    <test>
+      <!-- Based on the tests coming along with SPAdes -->
+      <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" />
+      <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
+      <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
+    </test>
+  </tests>
+  <help>
+**What it does**
+
+Runs SPAdes 2.5.0, collects the output, and throws away all the temporary files.
+
+**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. 
+    
+  </help>
+</tool>
diff -r 334ed4f2a504 -r 095f988dd814 tools/spades_2_5/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/spades_2_5/tool_dependencies.xml	Fri Aug 02 13:17:26 2013 -0500
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="spades" version="2.5.0">
+        <install version="1.1">
+            <actions>
+                <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.0/SPAdes-2.5.0-Linux.tar.gz</action>
+                <!-- Copying the whole bin folder -->
+		<action type="make_directory">$INSTALL_DIR/bin</action>
+		<action type="make_directory">$INSTALL_DIR/share</action>
+		<action type="move_directory_files">
+		  <source_directory>bin</source_directory>
+		  <destination_directory>$INSTALL_DIR/bin</destination_directory>
+		</action>
+                <action type="move_directory_files">
+		  <source_directory>share</source_directory>
+		  <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'/" $INSTALL_DIR/bin/spades.py</action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+This installs SPAdes 2.5.0.
+
+See manual here http://spades.bioinf.spbau.ru/release2.5.0/manual.html
+See also here http://bioinf.spbau.ru/en/spades
+        </readme>
+    </package>
+</tool_dependency>
+